Mass spectrometry-cleavable cross-linking agents

ABSTRACT

Provided herein is synthesis of novel mass spectrometry-cleavable cross-linking agents. The novel mass spectrometry-cleavable cross-linking agents can be used in mass spectrometry, tandem mass spectrometry, and multi-stage tandem mass spectrometry to facilitate structural analysis of intra-protein interactions in proteins and inter-protein interactions in protein complexes. Also provided are methods of mapping intra-protein interactions in proteins and inter-protein interactions in protein complexes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation-in-Part Application of U.S. application Ser. No. 14/927,332, filed Oct. 29, 2015, which is Continuation Application of U.S. application Ser. No. 13/471,365, filed May 14, 2012, and issued as U.S. Pat. No. 9,222,943 on Dec. 29, 2015, which claims the benefit of U.S. Provisional Application No. 61/486,260, filed May 14, 2011, which are hereby incorporated by reference in their entirety. This Continuation-in-Part Application claims the benefit of U.S. Provisional Application No. 62/222,690, filed Sep. 23, 2015, which is hereby incorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under Grant No. R01GM074830 awarded by the National Institutes of Health, Grant No. R21CA161807 awarded by the National Institutes of Health, and Grant No. R01GM106003 awarded by the National Institutes of Health. The Government has certain rights in this invention.

SEQUENCE LISTING IN ELECTRONIC FORMAT

The present application is being filed along with a Sequence Listing as an ASCII text file via EFS-Web. The Sequence Listing is provided as a file entitled UCI012001P1SEQLIST.txt, created and last saved on Dec. 5, 2016, which is 88,797 bytes in size. The information in the electronic format of the Sequence Listing is incorporated herein by reference in its entirety in accordance with 35 U.S.C. §1.52(e).

FIELD

The disclosure relates generally to cross-linking agents and methods of using cross-linking agents to facilitate structural analysis of proteins and protein complexes. In some embodiments, the disclosure relates to MS-cleavable cross-linking agents that are diester derivatives of 3,3′-sulfinylbispropanoic acid and methods of using MS-cleavable cross-linking agents that are diester derivatives of 3,3′-sulfinylbispropanoic acid to facilitate structural analysis of proteins and protein complexes.

In some embodiments, the disclosure relates to azide-tagged, acid-cleavable disuccinimidyl-bisulfoxide (azide-A-DSBSO) cross-linking agent and methods of using azide-A-DSBSO to facilitate structural analysis of proteins and protein complexes.

In some embodiments, the disclosure relates to alkyne-tagged, acid-cleavable disuccinimidyl-bisulfoxide (alkyne-A-DSBSO) cross-linking agent and methods of using alkyne-A-DSBSO to facilitate structural analysis of proteins and protein complexes.

BACKGROUND

Knowledge of elaborate structures of protein complexes is fundamental for understanding their functions and regulations. Although cross-linking coupled with mass spectrometry (MS) has been presented as a feasible strategy for structural elucidation of large multi-subunit protein complexes, this method has proven challenging due to technical difficulties in unambiguous identification of cross-linked peptides and determination of cross-linked sites by MS analysis.

Despite the availability of multiple types of MS-cleavable cross-linkers, most of the applications have been limited to the study of model peptides and single proteins. Additionally, complicated synthesis and fragmentation patterns have impeded most of the known MS-cleavable cross-linkers from wide adaptation by the community.

SUMMARY

In some embodiments, an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided. In some embodiments, the MS-cleavable cross-linker comprises at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group and at least one collision-induced dissociation (CID) cleavable bond.

In some embodiments of the MS-cleavable cross-linker, the amine-reactive NHS ester group is designed to react with a lysine side chain in a peptide or a protein. In some embodiments of the MS-cleavable cross-linker, the at least one CID cleavable bond is a sulfoxide bond. In some embodiments of the MS-cleavable cross-linker, the MS-cleavable cross-linker is DSSO, comprising the structure:

In some embodiments, the MS-cleavable cross-linker additionally comprises at least one enrichment handle and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.

In some embodiments of the MS-cleavable cross-linker, the at least one enrichment handle comprises a functional group, wherein the functional group is an azide functional group or an alkyne functional group, and wherein the functional group is designed for a click reaction with strained alkynes or a CuAAC reaction.

In some embodiments of the MS-cleavable cross-linker, the acid cleavable site is an acid labile acetal bond, wherein the acid labile acetal bond is designed to be cleaved under aqueous acidic conditions.

In some embodiments, wherein the MS-cleavable cross-linker is azide-A-DSBDO, comprising the structure:

In some embodiments, the MS-cleavable cross-linker is alkyne-A-DSBDO, comprising the structure:

In some embodiments, a method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided.

In some embodiments, the method comprises the steps of:

(i) providing 3,3′-thiodipropionic acid;

(ii) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-thiodipropionate from the compound of step (i); and

(iii) deriving DSSO from the compound of step (ii).

In some embodiments, a method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided.

In some embodiment, the method comprises the steps of:

(i) providing 2,2-bis(hydroxymethyl)propane-1,3-diol;

(ii) deriving (1,5-dioxaspiro[5.5]undecane-3,3-diyl)dimethanol from the compound of step (i);

(iii) deriving (1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene) dimethanesulfonate from the compound of step (ii);

(iv) deriving S,S′-((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene)) diethanethioate from the compound of step (iii);

(v) deriving dimethyl 3,3′-(((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (iv);

(vi) deriving dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate from the compound of step (v);

(vii) deriving dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (vi);

(viii) deriving 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionic acid from the compound of step (vii);

(ix) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (viii);

(x) deriving azide-A-DSBDO from the compound of step (ix).

In some embodiments, a method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided.

In some embodiment, the method comprises the steps of:

(i) providing 2,2-bis(bromomethyl)propane-1,3-diol and methyl 3-mercaptopropanoate;

(ii) deriving dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate from the compounds of step (i);

(iii) deriving dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (ii);

(iv) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (iii); and

(v) deriving azide-A-DSBDO from the compound of step (iv).

In some embodiments, a method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided.

In some embodiment, the method comprises the steps of:

(i) providing dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate;

(ii) deriving dimethyl 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (i);

(iii) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionatefrom the compound of step (ii); and

(iv) deriving alkyne-A-DSBDO from the compound of step (iii).

In some embodiments, a method for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof is provided. In some embodiment, the method comprises the steps of providing an MS-cleavable cross-linker, wherein the MS-cleavable cross-linker comprises at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group and at least one collision-induced dissociation (CID) cleavable bond, forming a cross-linked protein or protein complex by cross-linking the protein or the protein complex with the MS-cleavable cross-linker, forming one or more peptide fragments that are chemically bound to the MS-cleavable cross-linker by digesting the cross-linked protein or protein complex with an enzyme, and identifying the one or more peptide fragments using tandem mass spectrometry (MS^(n)), thereby mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex.

In some embodiments of the method, the MS-cleavable cross-linking agent is a derivative of a compound of structure:

wherein X is selected from the group consisting of:

wherein R is H, methyl or ethyl.

In some embodiments of the method, the MS-cleavable cross-linking agent is DSSO, comprising the structure:

In some embodiments of the method, the MS-cleavable cross-linking agent additionally comprises at least one enrichment handle, and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.

In some embodiments of the method, the MS-cleavable cross-linking agent is azide-A-DSBSO, comprising the structure:

In some embodiments of the method, the MS-cleavable cross-linking agent is alkyne-A-DSBSO, comprising the structure:

In some embodiments of the method, the at least one enrichment handle comprises a functional group for an enrichment strategy, wherein the functional group is an azide functional group or an alkyne functional group, and wherein the functional group is designed for a click reaction with strained alkynes or a CuAAC reaction.

In some embodiments of the method, the enrichment strategy is an affinity purification wherein the affinity purification comprises direct coupling with alkyne or azide functionalized beads or linking with one or more common affinity ligands such as biotin.

In some embodiments of the method, the acid cleavable site is an acid labile acetal bond, wherein the acid labile acetal bond is designed to be cleaved under aqueous acidic conditions for selective elution from an affinity column.

In some embodiments, a method for cross-linking mass spectrometry (XL-MS) for identifying one or more cross-linked peptides is provided. In some embodiments, the method comprises performing cross-linking with an MS-cleavable cross-linker to obtain one or more cross-linked proteins, wherein the MS-cleavable cross-linker comprises at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group, and at least one collision-induced dissociation (CID) cleavable bond, digesting the one or more cross-linked proteins with trypsin to obtain one or more cross-linked peptides, performing a liquid chromatography-tandem mass spectrometry (LC-MS^(n)) analysis on the one or more cross-linked peptides, wherein the LC-MSn analysis comprises detecting the one or more cross-linked peptides by MS 1 analysis, selecting the one or more cross-linked peptides detected by MS1 for MS2 analysis, selectively fragmenting the at least one CID cleavable bond and separating the one or more cross-linked peptides during MS2 analysis, sequencing the one or more cross-linked peptides separated during MS2 analysis by MS3 analysis, and integrating data obtained during MS1, MS2 and MS3 analyses to identify the one or more cross-linked peptides.

In some embodiments of the method, the MS-cleavable cross-linking agent is DSSO, comprising the structure:

In some embodiments of the method, the MS-cleavable cross-linking agent additionally comprises at least one enrichment handle and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.

In some embodiments of the method, the MS-cleavable cross-linking agent is azide-A-DSBSO, comprising the structure:

In some embodiments of the method, MS-cleavable cross-linking agent is alkyne-A-DSBSO, comprising the structure:

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows exemplary Compounds 1 and 3-9 and General Structure 2 according to the invention.

FIG. 2 shows proposed fragmentation schemes of DSSO-cross-linked peptides. A, DSSO synthesis and structure. B-D, MS/MS fragmentation patterns of the three types of DSSO-cross-linked peptides: interlinked (B), dead end (C), and intralinked (D). E, conversion of a sulfenic acid-modified fragment to an unsaturated thiol-modified fragment after a water loss. F, mass relationships between MS/MS fragment ions shown in B-D and their parent ions. DCC, N,N′-dicyclohexylcarbodiimide; MCPBA, m-chloroperbenzoic acid.

FIG. 3 is an exemplary MS^(n) analysis of DSSO-cross-linked model peptides. A-E, MS^(n) analysis of the DSSO-interlinked Ac-IR7 (α-α). A, MS spectrum of α-α: [α-α]³⁺ (m/z 615.97³⁺) and [α-α]²⁺ (m/z 923.46²⁺). B and C, MS/MS spectra of [α-α]³⁺ (B) and [α-α]²⁺ (C) in which alkene (α_(A)) and sulfenic acid (α_(S)) fragments were detected. D and E, MS³ spectra of α_(A) (m/z 449.66²⁺) (D) and α_(S) (m/z 948.43) (E). F-I, MS^(n) analysis of DSSO-interlinked Ac-myelin (β-β). F, MS spectrum of β-β: [β-β]⁶⁺ (m/z 458.23⁶⁺), [β-β]⁵⁺ (m/z 549.68⁵⁺), and [β-β]4+ (m/z 686.84⁴⁺). G-I, MS/MS spectra of [β-β]⁶⁺ in which β_(A)/β_(T) pair was observed (G), [β-β]⁵⁺in which the β_(A)/β_(S) pair was observed (H), and [β-β]⁴⁺ in which β_(A)/β_(S) pair was observed (I). J-L, MS^(n) analysis of DSSO dead end-modified substance P peptide γ_(DN). J, MS spectrum of γ_(DN) (m/z 538.76²⁺). K, MS/MS spectrum of γ_(DN) in which two fragments, γ_(A) (m/z 478.03²⁺) and γ_(s) (m/z 502.95²⁺), were detected. L, MS³ spectrum of γ_(A) (m/z 478.03²⁺). Sequences of Ac-IR7, Ac-myelin, and substance P are Ac-IEAEKGR (SEQ ID NO: 2), Ac-ASQKRPSQRHG (SEQ ID NO: 6), and RPKPQQF (SEQ ID NO: 7), respectively.

FIG. 4 is an exemplary MS^(n) analysis of DSSO heterodimeric interlinked peptide of cytochrome c (α-β: Ac-GDVEKGKK (SEQ ID NO: 11) interlinked to KKGER (SEQ ID NO: 13)). A, MS/MS spectrum of [α-β]⁴⁺ (m/z 419.9716⁴⁺) in which two fragment pairs were observed: α_(A) (m/z 478.99²⁺)/β_(T) (m/z 352.40²⁺) and α_(T) (m/z 494.96²⁺/β_(A) (m/z 336.42²⁺). B, MS³ spectrum of α_(A) (m/z 478.99²⁺) in which detection of y₁-y₇ and b₂-b₇ determined the sequence unambiguously as Ac-GDVEK_(A)GKK (SEQ ID NO: 12). C, MS³ spectrum of β_(T) (m/z 352.40²⁺) in which detection of y₁-y₄, a₁, and b₂-b₇ ions determined the sequence unambiguously as K_(T)KGER (SEQ ID NO: 14). K_(A) is modified with the alkene moiety, and K_(T) is modified with the unsaturated thiol moiety.

FIG. 5 is an exemplary MS^(n) analysis of DSSO heterodimeric interlinked peptide of cytochrome c (α-β: HKTGPNLHGLFGR (SEQ ID NO: 16) interlinked to GKK). This peptide was detected in MS as triply charged [α-β]³⁺ (m/z 641.6730³⁺), quadruply charged [α-β]⁴⁺ (m/z 481.5069⁴⁺), and quintuply charged [α-β]⁵⁺ (m/z 385.4070⁵⁺) ions. A, MS/MS spectrum of [α-β]³⁺ (m/z 641.6730³⁺) in which two fragment pairs were observed: α_(A) (m/z 744.40²⁺)/β_(T) (m/z 418.21) and α_(T) (m/z 760.38²⁺)/β_(A) (m/z 386.24). B, MS/MS spectrum of [α-β]⁴⁺ (m/z 481.5069⁴⁺) in which two fragment pairs were observed: α_(A) (m/z 496.60³⁺)/β_(T) (m/z 418.21) and α_(T) (m/z 507.26³⁺)/β_(A) (m/z 386.24). C, MS/MS spectrum of [α-β]⁵⁺ (m/z 385.4070⁵⁺) in which two fragment pairs were observed: α_(A)/β_(T) (m/z 496.60³⁺/209.61²⁺ and 372.70⁴⁺/418.21) and α_(T) (m/z 507.26³⁺)/β_(A) (m/z 193.62²⁺). D, MS³ spectrum of α_(A) fragment (m/z 496.60³⁺) in which detection of a series of y and b ions determined its sequence unambiguously as HK_(A)TGPNLHGLFGR (SEQ ID NO: 17). K_(A) is modified with the alkene moiety.

FIG. 6 is an exemplary MS^(n) analysis of DSSO dead end-modified peptide (A and B) and intralinked peptide of cytochrome c (C and D). A, MS/MS spectrum of a dead end-modified peptide (α_(DN); m/z 880.8975²⁺, K_(DN)TGQAPGFSYTDANK (SEQ ID NO: 20)) in which two fragment ions were determined as α_(A) (m/z 820.20²⁺) and α_(T) (m/z 835.88²⁺). B, MS³ spectrum of α_(A) (m/z 820.20²⁺) in which detection of a series of y and b ions determined its sequence unambiguously as K_(A)TGQAPGFSYTDANK (SEQ ID NO: 21). C, MS/MS spectrum of an intralinked peptide (α_(intra); m/z 611.9802³⁺, GGK*HK*TGPNLHGLFGR (SEQ ID NO: 24)) in which one fragment ion was observed and determined as α_(A+T) (m/z 606.24³⁺). D, MS³ spectrum of α_(A+T) (m/z 606.24³⁺) in which detection of a series of y and b ions determined the presence of a mixture of GGK_(A)HK_(T)TGPNLHGLFGR (SEQ ID NO: 25) and GGK_(T)HK_(A)TGPNLHGLFGR (SEQ ID NO: 26). K_(A) is modified with the alkene moiety, and K_(T) is modified with the unsaturated thiol moiety.

FIG. 7 shows A, the integrated data analysis work flow for identifying DSSO-crosslinked peptides by LC MS^(n) and B, the work flow for the Link-Finder program.

FIG. 8 is an exemplary MS^(n) analysis of DSSO heterodimeric interlinked peptide of the yeast 20 S proteasome complex (α-β: NKPELYQIDYLGTK (SEQ ID NO: 27) interlinked to LGSQSLGVSNKFEK (SEQ ID NO: 29)) with intersubunit link between 20 S subunit β4 and β3. A, MS/MS spectrum of [α-β]⁴⁺ (m/z 833.9231⁴⁺) in which two fragment pairs were detected and determined as α_(A) (m/z 868.52²⁺)/β_(T) (m/z 790.55²⁺) and α_(T) (m/z 884.98²⁺)/β_(A) (m/z 774.32²⁺). B, MS³ spectrum of α_(A) (m/z 868.52²⁺) in which detection of a series of y and b ions determined its sequence unambiguously as NK_(A)PELYQIDYLGTK (SEQ ID NO: 28). C, MS³ spectrum of β_(T) (m/z 790.55²⁺) in which detection of a series of y and b ions determined its sequence unambiguously as LGSQSLGVSNK_(T)FEK (SEQ ID NO: 30). K_(A) is modified with the alkene moiety, and K_(T) is modified with the unsaturated thiol moiety.

FIG. 9 shows a mapping identified DSSO-interlinked lysines onto crystal structure of yeast 20 S proteasome. The lysines forming intrasubunit cross-links appear space-filled in blue, and those forming intersubunit cross-links appear space-filled in red.

FIG. 10 is a flowchart showing a general technique for identifying crosslinked peptides according to one embodiment of the invention.

FIG. 11 is an exemplary SDS-PAGE gel picture of the 20S proteasome cross-linked with various molar ratios of cross-linker DSSO, i.e. 1:100, 1:500 and 1:1000. The 20S proteasome without cross-linking served as a control. The cross-linked proteasome complex was separated using 4-20% gradient gel.

FIG. 12 is an exemplary MS^(n) analysis of a DSSO dead-end peptide of the yeast 20S proteasome complex. A) MS/MS spectrum of a dead-end (DN) peptide (α_(DN), m/z 693.0078³⁺, AELEK_(DN)LVDHHPEGLSAR (SEQ ID NO: 110)), in which two fragment ions were determined as αA (m/z 652.67³⁺) and α_(T) (m/z 663.33³⁺); B) MS³ spectrum of α_(A) (m/z 652.67³⁺), detection of a series of y and b ions determined its sequence unambiguously as AELEK_(A)LVDHHPEGLSAR (SEQ ID NO: 111), in which K_(A) is modified with the alkene moiety. The sequence matched to subunit α7; C) MS3 spectrum of αT (m/z 663.33³⁺), detection of a series of y and b ions determined its sequence unambiguously as AELEK_(T)LVDHHPEGLSAR (SEQ ID NO: 112), in which K_(T) is modified with the unsaturated thiol moiety.

FIG. 13 shows CID cleavable cross-linker DSSO is based on the sulfoxide functional group. The arrow points to the bond that is broken during the CID process. A workflow for cross-linking proteins is shown. After protein cross-linking, trypsin digest generates the cross-linked peptide for LC/MS^(n) analysis. CID leads to selective cleavage of the bonds adjacent to the sulfoxide functional group.

FIG. 14 shows protein cross-linkers designed with CID cleavable sulfoxide groups. azide (3) or alkyne (4) groups for click chemistry enrichment strategies, and an acid labile acetal to facilitate affinity purification.

FIG. 15 shows an embodiment of a scheme for the synthesis of azide-A-DSBSO.

FIG. 16 shows an embodiment of a scheme for the synthesis of azide-A-DSBSO.

FIG. 17 shows an embodiment of a scheme for the synthesis of 5-azidopentan-2-one.

FIG. 18 shows an embodiment of a scheme for the synthesis of alkyne-A-DSBSO.

FIG. 19A-FIG. 19D show data for MS^(n) analysis of azide-A-DSBSO cross-linked Ac-myelin synthetic peptide.

FIG. 19A shows schematic illustration of MS² analysis of a azide-A-DSBSO interlinked homodimeric peptide (α-α). During collision-induced dissociation in MS², cleavage of either of the two symmetric MS-cleavable C—S bonds leads to physical separation of the two inter-linked peptides, thus generating pairs of peptide fragments: i.e. α_(A) and α_(T).

FIG. 19B shows the interlinked Ac-myelin was detected as multiple charged ions (m/z 1001.82³⁺, m/z 751.62⁴⁺, m/z 601.45⁵⁺, m/z 501.41⁶⁺.

FIG. 19C shows one of the two predicted peptide fragment pairs observed as α_(T) ²⁺/β_(A) ²⁺ (m/z 675.35²⁺/819.89²⁺).

FIG. 19D shows the second of the two predicted peptide fragment pairs observed as α_(T) ³⁺/β_(A) ³⁺ (449.90³⁺/546.93³⁺).

FIG. 20 shows an embodiment of a workflow for affinity purification of cross-linked cytochrome C proteins. The MS² fragments resulting from CID cleavage sites are shown.

FIG. 21A-FIG. 21D show MS^(n) analysis of a representative DSBSO 3 inter-linked peptide (α-β) of cytochrome C (m/z 510.02⁴⁺).

FIG. 21A shows MS¹ spectrum of the selected peptide.

FIG. 21B shows MS² spectrum of the selected peptide. In MS² spectrum, two pairs of peptide fragments: i.e. α_(A)/β_(T) (m/z 430.75²⁺/580.28²⁺) and α_(T)/β_(A) (m/z 521.752+/1489.282+) were detected. Note: α_(A), β_(A), and K_(A) are alkene modified species (+54 Da); α_(T) and β_(T) are unsaturated thiol modified species (+236 Da).

FIG. 21C shows MS³ spectra of α_(A) (m/z 430.75²⁺) fragments detected in MS². The detection of a series of y and b ions has unambiguously identified its sequences as KAYIPGTK.

FIG. 21D shows MS³ spectra of β_(A) (489.28²⁺) fragment detected in MS². The detection of a series of y and b ions has unambiguously identified its sequences as Mox1FAGIKAK. Mox: oxidized methionine.

FIG. 22 shows an embodiment of a synthesis scheme of a novel cross-linking reagent, Azide-A-DSBSO.

FIG. 23 shows an embodiment of azide-A-DSBSO-based in vivo XL-MS platform for mapping PPIs in living cells. Path I: at the proteome scale. Path II: at the targeted protein complex level. The inset displays structures of Azide-A-DSBSO and BARAC.

FIG. 24A-FIG. 24C show MS^(n) analysis of a representative DSBSO interlinked peptide (α-β) from in vivo cross-linked human 293 cells.

FIG. 24A shows graphic illustration of characteristic fragmentation of a DSBSO interlinked peptide (α-β) during collision-induced dissociation (CID) in MS2 at the top. At the bottom are shown MS1 and MS2 spectra of the representative cross-linked peptide (m/z 869.15524+). In the MS2 spectrum, two pairs of peptide fragments (i.e. αA/βT (m/z 590.312+/1139.502+) and αT/βA (681.312+/1048.002+)) were detected. αA, βA, and KA are alkene modified species (+54 Da); αT and βT are unsaturated thiol modified species (+236 Da).

FIG. 24B shows respective MS3 spectra of αA (m/z 590.312+) and PA (1048.002+) fragments detected in MS2. The detection of a series of y and b ions unambiguously identified their sequences as FANYIDKAVR and QKAQASHAQLGDAYDQEIR, respectively.

FIG. 24C shows integration of MS^(n) data identified this peptide as a DSBSO interlinked peptide (i.e. [FANYIDK120VR] cross-linked to [QK139QASHAQLGDAYDQEIR]).

FIG. 25 shows three sample preparation strategies for analyzing in vivo Azide-A-DSBSO cross-linked human 293 cells. Biotin conjugation with BARAC on the protein level (Paths I and II) and on the peptide level (Path III) for subsequent enrichment. Path I, BARAC conjugation after cell lysis; Path II, BARAC conjugation after cell fractionation (C=cytosolic; M=membrane; N=nuclear; I=insoluble fractions); Path III, BARAC conjugation and enrichment of cross-linked peptides after 100-kDa and 30-kDa ultrafiltration and digestion

FIG. 26A-FIG. 26D show MS^(n) analysis of a representative DSBSO interlinked peptide of in vivo cross-linked proteasome subunits. Integration of MS^(n) data identified this peptide as an intersubunit interlink between Rpt3 and Rpt6. KA, alkene modified lysine; KT, unsaturated thiol modified lysine.

FIG. 26A shows MS¹ spectrum of a representative DSBSO interlinked peptide [α-β] (m/z 659.82594+).

FIG. 26B shows MS² spectrum of [α-β] (m/z 659.82594+) in which interlinked peptide [α-β] was separated into fragment ions α_(A) (m/z 499.272+), β_(A) (m/z 720.372+), and β_(T) (m/z 811.372+).

FIG. 26C shows MS³ spectra of αA fragment ion which identified it as peptide NELNAKAVR of proteasome subunit Rpt6.

FIG. 26D shows MS³ spectra of βT fragment ion which identified it as peptide EFLHAQEEVKTR of proteasome subunit Rpt3.

FIG. 27A & FIG. 27B show optimization of biotin-conjugation and subsequent affinity purification using Azide-A-DSBSO cross-linked cytochrome C.

FIG. 27A shows Western blot analysis of biotin-conjugated products of Azide-A-DSBSO cross-linked cytochrome C after reacting with increasing amounts of BARAC. The effectiveness of biotin conjugation of Azide-A-DSBSO cross-linked cytochrome C and subsequent purification by binding to streptavidin resins was monitored by SDS-PAGE and immunoblotting. Top: reaction in phosphate buffer conditions; Bottom: reaction in 8M urea lysis buffer conditions. Western blots are probed with streptavidin-conjugated to HRP.

FIG. 27B shows Assessment of CytC cross-linking, biotin-conjugation, and streptavidin enrichment under optimal conditions by SDS-PAGE analysis and Coomassie blue staining. Different membranes were tested for their capabilities of handling cross-linked samples, the boxed region shows the same sample that was filtered with 3 different filter membranes; last two lanes were loaded at a 1:10 dilution in order to compare equivalent amounts of biotinconjugated CytC before (original load) and after (flow thru) binding to streptavidin beads.

FIG. 28A-FIG. 28C show optimization of BARAC conjugation and affinity purification on lysates of in vivo azide-A-DSBSO cross-linked human 293 cells.

FIG. 28A shows Western blot analysis of click chemistry reaction with Azide-A-DSBSO cross-linked 293 cell lysate and increasing amounts of BARAC (1-1000 μM).

FIG. 28B shows Western blot analysis of streptavidin binding efficiency using increasing ratios of lysate to streptavidin beads.

FIG. 28C shows Evaluation of biotin-conjugation and streptavidin binding efficiency of cross-linked lysate by immunoblotting. Samples were loaded in the following order: cross-linked lysate, biotin-conjugated crosslinked lysate, flow thru of biotin-conjugated cross-linked lysate after binding to streptavidin, and washes of streptavidin beads. XL=Cross-linked; FT=Flow Thru.

FIG. 29A-FIG. 29E show optimization of biotin-conjugation and affinity purification on cell fractionated and size fractionated in vivo azide-A-DSBSO cross-linked 293 cell lysates.

FIG. 29A shows SDS-PAGE analysis of non-crosslinked 293 cell fractions [C=Cytosolic; M=Membrane; N=Nuclear; I=Insoluble].

FIG. 29B shows SDS-PAGE analysis of Azide-ADSBSO cross-linked 293 cell lysate and cell fractions. [“-”=No fractionation].

FIG. 29C shows Western blot analysis of 293 cell lysate and cell fractions. Top: probed with calnexin antibody (membrane protein); Middle: probed with GAPDH antibody (cytosolic protein); Bottom: probed with Lamin A/C antibody (nuclear protein).

FIG. 29D shows 293 cell lysates reacted with increasing amounts of BARAC (0, 1, 10, 50, 100, 250. 500, 1000 μM), separated by SDS-PAGE and analyzed by Western blot probing for Streptavidin-HRP.

FIG. 29E shows dot blot of 100 and 30 kDa filtered lysates; [Bio-D=biotin-conjugated digest; S-FT=streptavidin flow thru].

FIG. 30 shows azide-A-DSBSO Cross-link Derived Protein-Protein Interaction Network from 293 Cells. Proteins are represented by a single node and interactions between proteins as a single edge. Edge thickness represents the number of inter-links (redundant and unique) captured and identified for a given interactions. Purple edges represent interactions also found in the IDB (Interaction Database) network. Nodes with shared/homologous peptides are grouped (H2A and H2B).

FIG. 31A-FIG. 31E show identified Intra- and Inter-Subunit Inter-Linked Peptides, Mapped onto 2.5 Å Nucleosome Crystal Structure Containing Histone H2A, H2B, H3.2, and H4. Visualization and distance measurements (in Å) were done with Pymol.

FIG. 31A shows nucleosome crystal structure downloaded from the Protein Data Bank (PDB); PDB ID=3AV1. Nucleosome complex consists of two copies each of Histone H2A (Blue), H2B (Green), H3.2 (Purple), and H4 (Red). Azide-A-DSBSO intra-subunit (yellow) and inter-subunit (black) inter-linked peptides are represented by dashed lines.

FIG. 31B shows zoomed in views of identified intra-subunit inter-links between H2BLys35-Lys58 and H2BLys35-Lys86 (black=dimer; red=monomer).

FIG. 31C shows zoomed in views of identified inter-subunit inter-links between H4Lys78-H2BLys86, H4Lys92-H2ALys37, H2ALys37-H2BLys35, and H2ALys37-H2BLys86.

FIG. 31D shows zoomed in views of identified inter-subunit inter-links between H3 .2Lys80-H4Lys78, H3 .2Lys80-H2BLys 109, H2BLys109-H4Lys60, and H2B 109-H2ALys96.

FIG. 31E shows zoomed in views of identified inter-subunit inter-links between H2ALys 119-H3.2Lys 123.

FIG. 32A & FIG. 32B show evaluation of HB-tag Based Tandem Affinity Purification of In Vivo Azide-ADSBSO Cross-linked Proteasome Complexes. Lanes: 1-cell lysate; 2-Flow through after the first step purification by binding to Ni-sepharose beads; 3-Elution from Ni-sepharose resins; 4-Flow through after second step purification by binding to streptavidin beads. Streptavidin-HRP was used to probe HB tagged proteasome subunits.

FIG. 32A shows evaluation of HB-tag Based Tandem Affinity Purification of In Vivo Azide-ADSBSO Cross-linked Proteasome Complexes from 293^(HB-Rpn11) cells.

FIG. 32B shows evaluation of HB-tag Based Tandem Affinity Purification of In Vivo Azide-ADSBSO Cross-linked Proteasome Complexes from 293^(HB-Rpt6) cells.

DESCRIPTION OF THE TABLES

TABLE 1—Summary of DSSO-interlinked peptides of cytochrome c identified by LC MSn.

TABLE 2—Summary of DSSO-interlinked peptides of the yeast 20 S proteasome complex identified by LC MSn.

TABLE 3—Summary of DSSO cross-linked peptides—DSSO dead-end, intra-linked and multilinked peptides—of cytochrome c by LC MSn.

TABLE 4—Summary of DSSO cross-linked peptides of ubiquitin by LC

MSn.

TABLE 5—Summary of DSSO inter-linked and dead-end peptides of the yeast 20S proteasome complex by LC MSn.

TABLE 6—Peptide sequences with their corresponding SEQ ID NOs.

TABLE 7—Summary of unique inter-linked peptides identified from azide-A-DSBSO cross-linked cytochrome C.

TABLE 8—Summary of proteins identified from in vivo cross-linked human 293 cells after enrichment.

TABLE 9—GO analysis of the identified azide-A-DSBSO cross-linked proteins.

TABLE 10—Detailed report of inter-linked peptides identified from in vivo cross-linked human 293 cells.

TABLE 11—Summary of identified inter-subunit inter-links of in vivo cross-linked proteasome complexes.

TABLE 12—Detailed summary of identified inter-subunit inter-linked peptides of in vivo cross-linked proteasome complexes.

TABLE 1 m/z AA MS m/z Δ Mod sequenced in Distance Type Peptide Sequence Location (Observed) z (PPM) Position MS3 z (Ca-Ca) References 2 Ac-GDVEKGK (SEQ ID G1-K7 565.30 3 1 K_(T)5 860.38 1  5.3 Å 19, 20, 21, 31 NO: 32) KIFVQK (SEQ ID NO: 35) K8-K13 K_(A)8 408.75 2 2 Ac-GDVEKGK (SEQ ID G1-K7 603.81 2 0 K_(A)5 828.41 1 13.0 Å 21, 31, 43 NO: 32) KK K87-K88 K87* 2 Ac-GDVEKGK (SEQ ID G1-K7 516.93 3 0 K_(T)5 860.38 1 13.0 Å 21, 31 NO: 32) KKGER (SEQ ID NO: 13) K87-R91 K_(A)87 336.20 2 2 Ac-GDVEKGK (SEQ ID G1-K7 474.23 3 2 K_(A)5 414.71 2 13.0 Å — NO: 32) KGER (SEQ ID NO: 38) K88-R91 K88* 2 Ac-GDVEKGK (SEQ ID G1-K7 675.35 3 4 K_(T)5 860.38 1 13.2 Å — NO: 32) EDLIAYLKK (SEQ ID NO: E92-K100 K_(A)99 573.83 2 39) 2 Ac-GDVEKGKK (SEQ ID G1-K8 445.57 3 1 K_(A)7 478.76 2 15.7 Å 21, 31 NO: 11) KK K87-K88 K87* 2 Ac-GDVEKGKK (SEQ ID G1-K8 419.97 4 0 K_(A)7 478.76 2 15.7 Å 21, 31 NO: 11) KKGER (SEQ ID NO: 13) K87-K91 K_(T)87 352.18 2 2 GKK G6-K8 641.67 3 0 K7* 760.39 2 18.7 Å 14, 31, 43 HKTGPNLHGLFGR (SEQ H26-R38 K_(T)27 ID NO: 16) 2 GKK G6-K8 526.26 2 0 K7* 616.29 1  9.9 Å 21, 43 KATNE (SEQ ID NO: 42) K100-E104 K100* 2 KIFVQK (SEQ ID NO: 35) K8-K13 398.90 3 2 K_(T)8 424.74 2 14.8 Å 31 KK K87-K88 K87* 2 KIFVQK (SEQ ID NO: 35) K8-K13 384.97 4 2 K_(A)8 408.75 2 14.8 Å 31 KKGER (SEQ ID NO: 13) K87-R91 K_(T)87 352.18 2 2 KIFVQK (SEQ ID NO: 35) K8-K13 494.59 3 2 K_(A)8 408.75 2 13.7 Å 21, 31 KATNE (SEQ ID NO: 42) K100-E104 K100* 2 GGKHK (SEQ ID NO: 44) G23-K27 756.70 3 2 K_(T)25 612.29 1 19.3 Å — KTGQAPGFSYTDANK K39-K53 K_(A)39 819.89 2 (SEQ ID NO: 19) 2 KTGQAPGFSYTDANK K39-K53 945.47 3 3 K_(A)39 819.89 2 15.1 Å 31 (SEQ ID NO: 19) EDLIAYLKK (SEQ ID NO: E92-K100 K_(T)99 1178.62 1 39) 2 KTGQAPGFSYTDANK K39-K53 768.69 3 0 K_(T)39 835.88 2 18.0 Å 21, 31, 43 (SEQ ID NO: 19) KATNE (SEQ ID NO: 42) K100-E104 K100* 2 TGQAPGFSYTDANKNK T40-K55 1104.21 3 2 K_(T)53 892.90 2 11.6 Å 31 (SEQ ID NO: 46) YIPGTKMoxIFAGIK (SEQ Y74-K86 K_(A)79 1508.82 1 ID NO: 49) 2 KYIPGTK (SEQ ID NO: K73-K79 629.68 3 2 K_(T)73^(‡) 892.46 1 13.2 Å 31 51) MoxIFAGIKK (SEQ ID M80-K87 K_(T)68^(‡) 1009.52 1 NO: 54) 2 MIFAGIKK (SEQ ID NO: M80-K87 389.21 4 2 K_(T)86 497.27 2  6.4 Å 31 53) KGER (SEQ ID NO: 38) K88-R91 K88* 2 MoxIFAGIKK (SEQ ID M80-K87 393.21 4 2 K_(T)86 505.27 2  6.4 Å 31 NO: 54) KGER (SEQ ID NO: 38) K88-R91 K88* *Peptide fragments containing these sites were not sequenced by MS³. ^(‡)They were identified from different fragment pair ions by MS³. Note: All of the inter-linked peptides displayed characteristic fragment pairs and were identified by Batch-tag, MS-Bridge and Link-Finder.

TABLE 2 m/z AA MS m/z Δ Mod. sequenced Distance Type Peptide Sequence Subunit Location (Observed) z (PPM) Position in MS3 z (Ca-Ca) 2 ATATGPKQQEITTNLE α1 (PRS2/SCL1) A168-K187 595.10 5 2 K_(A)174 571.29 4 14.8 Å NHFK (SEQ ID NO: 66) KVPDK (SEQ ID NO: α1 (PRS2/SCL1) K58-K62 K_(T)58 672.34 1 68) 2 KVAHTSYK (SEQ ID α2 (PRE8) K91-K98 477.51 4 2 K_(T)91 510.25 2  5.1 Å NO: 70) VLVDKSR (SEQ ID α2 (PRE8) V84-R90 K_(A)88 435.76 2 NO: 72) 2 IFKPQEIK (SEQ ID α3 (PRE9) I229-K236 514.03 4 0 K_(T)231 544.80 2 14.2 Å NO: 74) LYKLNDK (SEQ ID α3 (PRE9) L66-K72 K_(A)68 474.26 2 NO: 76) 2 IHAQNYLKTYNEDIPVEI α3 (PRE9) I93-R113 904.47 4 1 K_(T)100 1307.68 2 10.6 Å LVR (SEQ ID NO: 78) YKTNLYK (SEQ ID β3 (PUP3) Y69-K75 K_(A)70 492.27 2 NO: 80) 2 EFLEKNYDR (SEQ ID α4 (PRE6) E173-R181 692.33 3 2 K_(A)177‡ 634.30 2 13.1 Å NO: 83) NSKTVR (SEQ ID NO: α4 (PRE6) N167-R172 K_(A)169‡ 379.71 2 85) 2 ILKQVMEEK (SEQ ID α5 (PUP2) I203-K211 641.01 3 0 K_(T)205 602.31 2 10.5 Å NO: 87) ELKEK (SEQ ID NO: α5 (PUP2) E242-K246 K244* 89) 2 SYKFPR (SEQ ID NO: β2 (PUP1)† S202-R207 539.26 3 1 K_(A)204 426.23 2 12.1 Å 90) EEKQK (SEQ ID NO: β2 (PUP1)† E197-K201 K_(T)199 747.34 1 92) 2 YKTNLYK (SEQ ID β3 (PUP3) Y69-K75 587.64 3 2 K_(A)70‡ 492.26 2 10.7 Å NO: 80) LKEER (SEQ ID NO: β3 (PUP3) L76-R80 K_(A)77‡ 364.70 2 94) 2 LGSQSLGVSNKFEK β3 (PUP3) L29-K42 595.05 4 2 K_(T)39 790.40 2 13.2 Å (SEQ ID NO: 29) YLKMoxR (SEQ ID β3 (PUP3) Y199-R203 K_(A)201 390.71 2 NO: 97) 2 NKPELYQIDYLGTK β4 (PRE1) N112-K125 833.92 4 0 K_(A)113 868.45 2 19.1 Å (SEQ ID NO: 27) LGSQSLGVSNKFEK β3 (PUP3) L29-K42 K_(T)39 790.39 2 (SEQ ID NO: 29) 2 VQDSVILASSKAVTR β4 (PRE1) V9-R23 633.74 5 1 K_(A)19 543.30 3  7.8 Å (SEQ ID NO: 99) GISVLKDSDDKTR β4 (PRE1) G24-R36 K_(T)29 760.38 2 (SEQ ID NO: 101) 2 FKNSVK (SEQ ID NO: β6 (PRE7)† F59-K64 532.29 3 2 K_(T)60 808.40 1 16.2 Å 103) KLAVER (SEQ ID NO: α6 (PRE5) K102-R107 K_(A)102 385.23 2 105) 2 NQYEPGTNGKVK β6 (PRE7)† N149-K160 659.68 3 0 K_(A)158 694.84 2  9.8 Å (SEQ ID NO: 106) KPLK (SEQ ID β6 (PRE7) † K161-K164 K161* NO: 108) * Peptide fragments containing these sites were not sequenced by MS³. ‡They were identified from different fragment pair ions by MS³. †Mature sequence from crystal data was used for data analysis. Note: All of the inter-linked peptides displayed characteristic fragment pairs and were identified by Batch-tag, MS-Bridge and Link-Finder.

TABLE 3 m/z Identified AA MS m/z Δ Mod. sequenced Peptide Expectation in Other Type Peptide Sequence Location (Observed) z (PPM) Position in MS3 z Score Value Refs 0 Ac-GDVEKGKK (SEQ ID G1-K8 539.76 2 1 K_(T)5 494.74 2 22.7 1.90E−05 21 NO: 11) 0 KIFVQK (SEQ ID K8-K13 469.76 2 2 K_(A)8 408.75 2 19.1 1.00E−04 19, 20, 21, NO: 35) 31 0 KTGQAPGFSYTDANK K39-K53 880.90 2 2 K_(T)39 835.88 2 41.5 2.10E−10 19, 20, 21, (SEQ ID NO: 19) 41 0 TGQAPGFSYTDANKNK T40-K55 937.92 2 0 K_(T)53 892.90 2 28.8 4.60E−08 19, 31 (SEQ ID NO: 46) 0 KYIPGTK (SEQ ID K73-K79 491.75 2 2 K_(A)73 430.75 2 23.9 1.40E−05 20, 21, 31 NO: 51) 0 YIPGTKMoxIFAGIK Y74-K86 815.92 2 2 K_(T)79 770.90 2 18.3 5.00E−06 19, 31 (SEQ ID NO: 49) 0 MoxIFAGIKK (SEQ M80-K87 550.28 2 1 K_(T)86 505.27 2 22.0 4.20E−06 31 ID NO: 54) 0 EDLIAYLKK (SEQ ID E92-K100 634.83 2 1 K_(A)99 573.83 2 32.9 2.70E−07 21, 31 NO: 39) m/z Ex- Identified Peptide AA MS m/z Δ Mod. sequenced Peptide pectation Distance in Type Sequence Location (Observed) z (PPM) Position in MS3 z Score Value (Ca-Ca) other Refs 1 Ac- G1-K8 530.75 2 2 K_(A)5, K_(T)7 521.75 2 19.5 6.20E−05  5.4 Å 21 GDVEKGK K (SEQ ID NO: 11) 1 GGKHKTG G23-R38 611.98 3 0 K_(A)25, K_(T)27 605.98 3 37.7 2.80E−08  6.3 Å 14, 19, 20, PNLHGLFG 21, 31, 42 R (SEQ ID NO: 23) 1 KYIPGTKM K73-K86 870.96 2 2 K73, K79* — — — 12.1 Å 31 oxIFAGIK (SEQ ID NO: 114) 1 KYIPGTKM K73-K87 623.67 3 2 K73, K86* — — — 13.2 Å 31 oxIFAGIKK (SEQ ID NO: 116) 1 MoxIFAGIK M80-K88 605.32 2 2 K_(A)86, K_(T)87 596.32 2 29.5 1.10E−08 — 14, 19, 20, KK (SEQ 21, 31, 42 ID NO: 118) 1 KKGER K87-R91 388.19 2 1 K_(A)87, K_(s)88* — — — — 20, 21 (SEQ ID NO: 13) 1 EDLIAYLKK E92-E104 833.41 2 3 K_(A)99, K_(T)100 824.40 2 28.7 1.50E−06 — 21, 31 ATNE (SEQ ID NO: 119) m/z Best Best Peptide AA MS m/z Δ Mod. sequenced Discovery Expectation Distance Type Sequence Location (Observed) z (PPM) Position in MS3 z Score Value (Ca-Ca) References 2 Ac- G1-K7 565.30 3 1 K_(T)5 860.38 1 19.7 2.70E−05  5.3 Å 19, 20, 21, GDVEKGK 31 (SEQ ID NO: 32) KIFVQK K8-K13 K_(A)8 408.75 2 20.3 1.90E−05 (SEQ ID NO: 35) 2 Ac- G1-K7 603.81 2 0 K_(A)5 828.41 1 23.1 2.70E−06 13.0 Å 21, 31, 43 GDVEKGK (SEQ ID NO: 32) KK K87-K88 K87* 2 Ac- G1-K7 516.93 3 0 K_(T)5 860.38 1 19.7 2.70E−05 13.0 Å 21, 31 GDVEKGK (SEQ ID NO: 32) KKGER K87-R91 K_(A)87 336.20 2 14.8 1.50E−04 (SEQ ID NO: 13) 2 Ac- G1-K7 474.23 3 2 K_(A)5 414.71 2 25.5 8.60E−07 13.0 Å — GDVEKGK (SEQ ID NO: 32) KGER K88-R91 K88* (SEQ ID NO: 38) 2 Ac- G1-K7 675.35 3 4 K_(T)5 860.38 1 19.7 2.70E−05 13.2 Å — GDVEKGK (SEQ ID NO: 32) EDLIAYLKK E92-K100 K_(A)99 573.83 2 32.9 2.10E−07 (SEQ ID NO: 39) 2 Ac- G1-K8 445.57 3 1 K_(A)7 478.76 2 23.1 7.50E−06 15.7 Å 21, 31 GDVEKGK K (SEQ ID NO: 11) KK K87-K88 K87* 2 Ac- G1-K8 419.97 4 0 K_(A)7 478.76 2 22.0 2.20E−05 15.7 Å 21, 31 GDVEKGK K (SEQ ID NO: 11) KKGER K87-K91 K_(T)87 352.18 2 15.5 1.40E−03 (SEQ ID NO: 13) 2 GKK G6-K8 641.67 3 0 K7* HKTGPNLH H26-R38 K_(T)27 760.39 2 35.0 7.10E−11 18.7 Å 14, 31, 43 GLFGR (SEQ ID NO: 16) 2 GKK G6-K8 526.26 2 0 K7*  9.9 Å 21, 43 KATNE K100- K_(A)100 616.29 1 14.2 2.40E−09 (SEQ ID E104 NO: 42) 2 KIFVQK K8-K13 398.90 3 2 K_(T)8 424.74 2 19.4 1.40E−04 14.8 Å 31 (SEQ ID NO: 35) KK K87-K88 K87* 2 KIFVQK K8-K13 384.97 4 2 K_(A)8 408.75 2 20.3 1.90E−05 14.8 Å 31 (SEQ ID NO: 35) KKGER K87-R91 K_(T)87 352.18 2 15.0 1.00E−04 (SEQ ID NO: 13) 2 KIFVQK K8-K13 494.59 3 2 K_(A)8 408.75 2 20.6 3.20E−05 13.7 Å 21, 31 (SEQ ID NO: 35) KATNE K100- K100* (SEQ ID E104 NO: 42) 2 GGKHK G23-K27 756.70 3 2 K_(T)25 612.29 1 9.0# 8.00E−03 19.3 Å — (SEQ ID NO: 44) KTGQAPG K39-K53 K_(A)39 819.89 2 44.7 5.70E−11 FSYTDANK (SEQ ID NO: 19) 2 KTGQAPG K39-K53 945.47 3 3 K_(A)39 819.89 2 42.5 2.50E−10 15.1 Å 31 FSYTDANK (SEQ ID K_(T)99 1178.62 1 22.9 1.80E−05 NO: 19) EDLIAYLKK E92-K100 (SEQ ID NO: 39) 2 KTGQAPG K39-K53 768.69 3 0 K_(T)39 835.88 2 39.9 1.20E−09 18.0 Å 21, 31, 43 FSYTDANK (SEQ ID NO: 19) KATNE K100- K100* (SEQ ID E104 NO: 42) 2 TGQAPGF T40-K55 1104.21 3 2 K_(T)53 892.90 2 28.8 4.60E−08 11.6 Å 31 SYTDANKN K (SEQ ID NO: 46) YIPGTKMo xIFAGIK Y74-K86 K_(A)79 1508.82 1 9.3# 1.00E−03 (SEQ ID NO: 49) 2 KYIPGTK K73-K79 629.68 3 2 K_(T)73‡ 892.46 1 17.6 2.00E−05 13.2 Å 31 (SEQ ID NO: 51) MoxIFAGIK M80-K87 K_(T)86‡ 1009.52 1 15.0 2.10E−05 K (SEQ ID NO: 54) 2 MIFAGIKK M80-K87 389.21 4 2 K_(T)86 497.27 2 18.9 5.00E−05  6.4 Å 31 (SEQ ID NO: 53) KGER K88-R91 K88* (SEQ ID NO: 38) 2 MoxIFAGIK M80-K87 393.21 4 2 K_(T)86 505.27 2 24.0 4.20E−07  6.4 Å 31 K (SEQ ID NO: 54) KGER K88-R91 K88* (SEQ ID NO: 38) m/z Ex- Identified Peptide AA MS m/z Δ Mod. sequenced Peptide pectation Distance in Type Sequence Location (Observed) z (PPM) Position in MS3 z Score Value (Ca-Ca) Other Refs 0.0 GGKHKTG G23-R38 507.74 4 −2 K_(A)25, K_(A)27 446.74 4 28.0 1.10E−06 — — PNLHGLFG R (SEQ ID NO: 23) 0.1 YIPGTKMo Y74-K88 682.34 3 1 K_(A)79, K_(A)86, 635.67 3 24.6 3.60E−05 — — xIFAGIKKK Kr87 (SEQ ID NO: 121) 0.1 MoxIFAGIK M80-R91 576.61 3 2 K_(A)86, K_(A)87, 529.94 3 31.8 1.20E−05 — — KKGER K_(T)88 (SEQ ID NO: 123) 0.1 MoxIFAGIK M80-R91 864.41 2 1 K_(T)86, K_(A)87, 794.41 2 34.0 2.00E−08 — — KKGER K_(A)88 (SEQ ID NO: 123) 0.2 Ac- G1-K8 899.40 2 1 K5, K7* ~11.3 Å — GDVEKGK K (SEQ ID NO: 11) KATNE K100- K_(A)100 616.29 1 14.2 2.60E−08 (SEQ ID E104 NO: 42) 0.2 GKK G6-K8 469.04 5 0 K7* ~18.7 Å — GGKHKTG G23-R38 K_(A)25, K_(A)27 446.74 4 22.3 4.20E−06 PNLHGLFG R (SEQ ID NO: 23) 0.2 GKKIFVQK G6-K13 519.28 3 2 K_(T)7, K_(A)8 544.30 2 23.1 1.90E−05 ~15.3 Å — (SEQ ID NO: 124) KK K87-K88 K87* 1.2 Ac- G1-K7 828.40 3 0 K_(T)5 860.38 1 19.5 3.20E−05 ~13.8 Å — GDVEKGK (SEQ ID NO: 32) MoxIFAGIK M80-R91 K_(A)86, K_(A)87, 794.41 2 36.3 2.00E−09 KKGER K_(T)88 (SEQ ID NO: 123) 1.2 Ac- G1-K13 799.06 3 2 K_(T)5, K_(T)7, 872.43 2 18.7 1.20E−04 ~12.1 Å — GDVEKGK K_(A)8 KIFVQK (SEQ ID NO: 126) KATNE K100- K_(A)100 616.30 1 14.2 2.40E−09 (SEQ ID E104 NO: 42) 1.2 KYIPGTK K73-K79 839.10 3 1 K_(T)73 892.46 1 17.6 2.00E−05 ~15.3 Å — (SEQ ID NO: 51) MoxIFAGIK M80-R91 K_(A)86 K_(T)87, 794.41 2 36.3 2.00E−09 KKGER K_(A)88 (SEQ ID NO: 123) 2.2 Ac- G1-K8 599.79 4 0 K5, K7* ~14.38 Å, — GDVEKGK ~11.3 Å K (SEQ ID NO: 11) KKGER K87-R91 K_(A)87 336.20 2 14.8 1.50E−04 (SEQ ID NO: 13) KATNE K100- K100* (SEQ ID E104 NO: 42) *Peptide fragments containing these sites were not sequenced by MS3. **These intra-linked were identified by MS/MS. #These MS3 data were considered due to the presence of other lines of evidence for identifying the cross-linked peptides. ‡They were identified from different charged fragment pair ions by MS3 Note: Type 0: dead-end Type 1: intra-linked Type0, 1; 0, 2; 1, 2, 2, 2: multi-linked All of the peptides displayed characteristic fragment pairs. All of the cross-linked peptides were identified by Link-Finder, Batch-tag and MS-Bridge.

TABLE 4 m/z Identified AA MS m/z Δ Mod. sequenced Peptide Expectation in Other Type Peptide Sequence Location (Observed) z (PPM) Position in MS3 z Score Value Refs 0 MQIFVKTLTGK (SEQ ID M1-K11 721.38 2 9 K_(T)6 676.36 2 30.1 5.40E−08 19, 38 NO: 127) 0 AKIQDK (SEQ ID NO: A28-K33 439.72 2 7 K_(T)29 394.71 2 18.0 2.40E−04 — 128) 0 LIFAGKQLEDGR (SEQ L43-R54 761.89 2 10 K_(T)48 716.87 2 35.1 1.10E−07 19, 38 ID NO: 60) 0 LIFAGKQLEDGRTLSDYNI L43-K62 862.44 3 8 K_(T)48 832.43 3 34.1 1.20E−07 — QK (SEQ ID NO: 129) 0 TLSDYNIQKESTLHLVLR T55-R72 769.40 3 10 K_(A)63 728.73 3 36.1 1.40E−07 19, 38 (SEQ ID NO: 64) m/z Pep- Identified Peptide AA MS m/z Δ Mod. sequenced tide Expectation Distance in Other Type Sequence Location (Observed) z (PPM) Position in MS2 z Score Value (Ca-Ca) Refs 1 AKIQDKEGIPP A28-R42 940.97 2 5 K29, K33 940.97 28.5 4.40E−07 6.42 Å 19 DQQR (SEQ ID NO: 130) 2 TLTGKTITLEVE T7-K27 993.01 4 5 K11* 13.3 Å 38 PSDTIENVK (SEQ ID NO: 57) IQDKEGIPPDQ I30-R42 K_(A)33 789.41 2 28.6 3.20E−08 QR (SEQ ID NO: 58) 2 LIFAGKQLEDG L43-R54 713.38 4 5 K_(A)48 700.88 2 39.2 1.00E−08 15.3 Å 19 R (SEQ ID NO: 319) LIFAGKQLEDG L43-R54 K_(T)48 716.87 2 36.4 1.90E−08 R (SEQ ID NO: 60) 2 LIFAGKQLEDG L43-R54 909.24 4 9 K_(A)48 700.89 2 35.5 1.80E−08 18.4 Å 19, 38 R (SEQ ID NO: 319) TLSDYNIQKES T55-R72 K_(T)63 1108.58 2 31.3 1.20E−08 TLHLVLR (SEQ ID NO: 443) *Peptide fragments containing these sites were not sequenced by MS3. Note: Type 0: dead-end Type 1: intra-linked Type 2: inter-linked All of the peptides displayed characteristic fragment pairs. All of the cross-linked peptides were identified by Link-Finder, Batch-tag and MS-Bridge.

TABLE 5 m/z AA MS m/z Δ Mod. sequenced peptide Expectation Type Peptide Sequence Subunit Location (Observed) z (PPM) Position in MS3 z Score Value 0 AKAEAAEFR (SEQ α1 A97-R105 584.77 2 −1 K_(T)98 539.75 2 35.0 1.50E−04 ID NO: 131) (PRS2/SCL1) 0 VLVDKSR (SEQ ID α2 (PRE8) V84-R90 496.76 2 0 K_(A)88 435.76 2 23.8 4.60E−04 NO: 72) 0 TFLEKR (SEQ ID α2 (PRE8) T173-R178 485.24 2 1 K_(A)177 424.24 2 22.9 3.30E−04 NO: 132) 0 KVTSTLLEQDTSTEK α3 (PRE9) K51-K65 928.45 2 0 K_(A)51 867.45 2 47.2 3.50E−09 (SEQ ID NO: 133) 0 STLKLQDTR (SEQ α4 (PRE6) S50-R58 619.31 2 1 K_(A)53 558.31 2 36.3 3.90E−05 ID NO: 134) 0 ITPSKVSK (SEQ ID α4 (PRE6) I59-K66 518.27 2 1 K_(T)63 473.26 2 21.3 2.30E−03 NO: 135) 0 ILIEKAR (SEQ ID α4 (PRE6) I84-R90 509.78 2 −1 K_(T)88 464.77 2 27.4 1.40E−03 NO: 136) 0 NSKTVR (SEQ ID α4 (PRE6) N167-R172 440.71 2 1 K_(T)176 395.70 2 22.1 5.90E−03 NO: 85) 0 EFLEKNYDR (SEQ α4 (PRE6) E173-R181 695.30 2 −1 K_(T)177 650.29 2 30.9 1.40E−05 ID NO: 83) 0 TAELIKELK (SEQ α5 (PUP2) T236-K244 610.82 2 −4 K_(T)241 565.81 2 36.3 1.80E−04 ID NO: 137) 0 KLAVER (SEQ ID α6 (PRE5) K102-R107 446.23 2 2 K_(A)102 385.23 2 18.1 3.00E−04 NO: 105) 0 LLVPQKNVK (SEQ α7 (PRE10) L58-K66 607.84 2 1 K_(T)63 562.83 2 24.2 9.20E−05 ID NO: 138) 0 AELEKLVDHHPEGL α7 (PRE10) A174-R190 693.00 3 −2 K_(T)178 663.00 3 33.5 6.70E−06 SAR (SEQ ID NO: 109) 0 EAVKQAAK (SEQ α7 (PRE10) E191-K198 510.76 2 2 K_(T)194 465.74 2 26.9 7.10E−04 ID NO: 139) 0 YKTNLYK (SEQ ID β3 (PUP3) Y69-K75 553.27 2 3 K_(T)70 508.25 2 25.7 9.60E−05 NO: 80) 0 TNLYKLK (SEQ ID β3 (PUP3) T71-K77 528.27 2 −5 K_(A)75 467.27 2 25.9 2.50E−03 NO: 140) 0 QELAKSIR (SEQ ID β4 (PRE1) Q86-R93 560.79 2 2 K_(A)90 499.79 2 22.5 4.00E−03 NO: 141) 0 IVDKDGIR (SEQ ID β4 (PRE1) I183-R190 546.27 2 1 K_(T)186 501.26 2 30.6 1.40E−03 NO: 142) 0 FKNSVK (SEQ ID β6 (PRE7)† F59-K64 449.72 2 1 K_(T)60 404.71 2 19.0 1.90E−02 NO: 103) 0 KLSINSAAR (SEQ β6 (PRE7)† K74-R82 568.29 2 3 K_(A)74 507.29 2 32.8 2.00E−04 ID NO: 143) 0 KEFYELK (SEQ ID β6 (PRE7)† K205-K211 566.77 2 2 K_(A)205 505.77 2 24.7 5.40E−03 NO: 144) m/z Expec- Peptide MS m/z Δ Mod. sequenced Peptide tation Distance Type Sequence Subunit AA Location (Observed) z (PPM) Position in MS3 z Score Value (Ca-Ca) 2 ATATGPKQQ α1 A168-K187 595.10 5 2 K_(A)174 571.29 4 24.5 2.90E−04 14.8 Å EITTNLENHF (PRS2/SCL1) K (SEQ ID NO: 66) KVPDK (SEQ α1 K58-K62 K_(T)58 672.34 1 12.3 0.71** ID NO: 68) (PRS2/SCL1) 2 KVAHTSYK α2 (PRE8) K91-K98 477.51 4 2 K_(T)91 510.25 2 29.9 7.60E−05  5.1 Å (SEQ ID NO: 70) VLVDKSR α2 (PRE8) V84-R90 K_(A)88 435.76 2 27.6 2.50E−03 (SEQ ID NO: 72) KVAHTSYK α2 (PRE8) K91-K98 382.21 5 1 K_(A)91 329.85 3 19.3 1.90E−02 (SEQ ID NO: 70) VLVDKSR α2 (PRE8) V84-R90 K_(T)88 451.74 2 25.4 2.50E−04 (SEQ ID NO: 72) 2 IFKPQEIK α3 (PRE9) I229-K236 514.03 4 0 K_(T)231 544.80 2 23.6 1.50E−02 14.2 Å (SEQ ID NO: 74) LYKLNDK α3 (PRE9) L66-K72 K_(A)68 474.26 2 25.5 5.50E−03 (SEQ ID NO: 76) 2 IHAQNYLKTY α3 (PRE9) I93-R113 904.47 4 1 K_(T)100 1307.68 2 26.6 7.90E−05 10.6 Å NEDIPVEILV R (SEQ ID NO: 78) YKTNLYK β3 (PUP3) Y69-K75 K_(A)70 492.27 2 23.9 3.00E−03 (SEQ ID NO: 80) IHAQNYLKTY α3 (PRE9) I93-R113 723.78 5 5 K100* NEDIPVEILV R (SEQ ID NO: 78) YKTNLYK β3 (PUP3) Y69-K75 K_(A)70 492.27 2 24.2 2.90E−03 (SEQ ID NO: 80) 2 EFLEKNYDR α4 (PRE6) E173-R181 692.33 3 2 K_(A)177^(‡) 634.30 2 23.6 2.60E−04 13.1 Å (SEQ ID NO: 83) NSKTVR α4 (PRE6) N167-R172 K_(A)169^(‡) 379.71 2 22.6 2.80E−03 (SEQ ID NO: 85) EFLEKNYDR α4 (PRE6) E173-R181 519.50 4 2 K_(T)177 650.29 2 33.2 1.70E−05 (SEQ ID NO: 83) NSKTVR α4 (PRE6) N167-R172 K_(A)169 379.71 2 22.6 2.80E−03 (SEQ ID NO: 85) 2 ILKQVMEEK α5 (PUP2) I203-K211 641.01 3 0 K_(T)205 602.31 2 29.2 3.50E−03 10.5 Å (SEQ ID NO: 87) ELKEK (SEQ α5 (PUP2) E242-K246 K244* ID NO: 89) ILKQVMEEK α5 (PUP2) I203-K211 481.01 4 0 K_(T)205 602.31 2 27.6 2.60E−04 (SEQ ID NO: 87) ELKEK (SEQ α5 (PUP2) E242-K246 K244* ID NO: 89) 2 SYKFPR β2 (PUP1)† S202-R207 539.26 3 1 K_(A)204 426.23 2 23.1 6.40E−03 12.1 Å (SEQ ID NO: 90) EEKQK (SEQ β2 (PUP1)† E197-K201 K_(T)199 747.34 1 10.4 0.33** ID NO: 92) SYKFPR β2 (PUP1)† S202-R207 404.70 4 2 K_(T)204 442.21 2 21.1 8.20E−04 (SEQ ID NO: 90) EEKQK (SEQ β2 (PUP1)† E197-K201 K199* ID NO: 92) 2 YKTNLYK β3 (PUP3) Y69-K75 587.64 3 2 K_(A)70^(‡) 492.26 2 23.8 4.60E−04 10.7 Å (SEQ ID NO: 80) LKEER (SEQ β3 (PUP3) L76-R80 K_(A)77^(‡) 364.70 2 17.0 2.70E−02 ID NO: 94) YKTNLYK β3 (PUP3) Y69-K75 440.98 4 2 K_(T)70 508.25 2 25.7 1.10E−04 (SEQ ID NO: 80) LKEER (SEQ β3 (PUP3) L76-R80 K_(A)77 364.70 2 16.5 8.40E−03 ID NO: 94) 2 LGSQSLGVS β3 (PUP3) L29-K42 793.07 3 2 K_(A)39 774.41 2 42.0 5.30E−07 13.2 Å NKFEK (SEQ ID NO: 29) YLKMoxR β3 (PUP3) Y199-R203 K_(T)201 406.69 2 16.2 1.10E−03 (SEQ ID NO: 97) LGSQSLGVS β3 (PUP3) L29-K42 595.05 4 2 K_(T)39 790.40 2 40.7 8.40E−07 NKFEK (SEQ ID NO: 29) YLKMoxR β3 (PUP3) Y199-R203 K_(A)201 390.71 2 18.1 6.10E−03 (SEQ ID NO: 97) 2 NKPELYQID β4 (PRE1) N112-K125 833.92 4 0 K_(A)113 868.45 2 32.0 9.50E−08 19.1 Å YLGTK (SEQ ID NO: 27) LGSQSLGVS β3 (PUP3) L29-K42 K_(T)39 790.39 2 26.5 3.90E−05 NKFEK (SEQ ID NO: 29) 2 VQDSVILASS β4 (PRE1) V9-R23 633.74 5 1 K_(A)19 543.30 3 23.0 4.90E−03  7.8 Å KAVTR (SEQ ID NO: 99) GISVLKDSD β4 (PRE1) G24-R36 K_(T)29 760.38 2 35.4 2.40E−05 DKTR (SEQ ID NO: 101) 2 FKNSVK β6 (PRE7)† F59-K64 532.29 3 2 K_(T)60 808.40 1 16.2 2.00E−02 16.2 Å (SEQ ID NO: 103) KLAVER α6 (PRE5) K102-R107 K_(A)102 385.23 2 21.2 9.80E−04 (SEQ ID NO: 105) FKNSVK β6 (PRE7)† F59-K64 399.47 4 2 K_(T)60 404.71 2 16.5 1.10E−02 (SEQ ID NO: 103) KLAVER α6 (PRE5) K102-R107 K_(A)102 385.23 2 18.3 1.60E−04 (SEQ ID NO: 105) 2 NQYEPGTN β6 (PRE7)† N149-K160 659.68 3 0 K_(A)158 694.84 2 29.8 4.20E−05  9.8 Å GKVK (SEQ ID NO: 106) KPLK (SEQ β6 (PRE7)† K161-K164 K161* ID NO: 108) NQYEPGTN β6 (PRE7)† N149-K160 495.01 4 2 K_(T)158 710.83 2 26.3 3.00E−04 GKVK (SEQ ID NO: 106) KPLK (SEQ β6 (PRE7)† K161-K164 K161* ID NO: 108) *Peptide fragment containing these sites were not sequenced by MS3 **The peptide identification was above 1% false positive rate but MS3 was validated manually. ‡They were identified from different fragment pair ions by MS3 †Mature sequence from crystal data was used for data analysis. Note: Type 0: dead-end All of the peptides displayed characteristic fragment pairs. All of the cross-linked peptides were identified by Link-Finder, Batch-tag and MS-Bridge.

TABLE 6 SEQ ID NO: Sequence SEQ ID NO: 1 IEAEKGR SEQ ID NO: 2 Ac-IEAEKGR SEQ ID NO: 3 Ac-IEAEK_(A)GR SEQ ID NO: 4 Ac-IEAEK_(S)GR SEQ ID NO: 5 ASQKRPSQRHG SEQ ID NO: 6 Ac-ASQKRPSQRHG SEQ ID NO: 7 RPKPQQF SEQ ID NO: 8 RPK_(A)PQQF SEQ ID NO: 9 RPK_(DN)PQQF SEQ ID NO: 10 GDVEKGKK SEQ ID NO: 11 Ac-GDVEKGKK SEQ ID NO: 12 Ac-GDVEK_(A)GKK SEQ ID NO: 13 KKGER SEQ ID NO: 14 K_(T)KGER SEQ ID NO: 15 K_(A)KGER SEQ ID NO: 16 HKTGPNLHGLFGR SEQ ID NO: 17 HK_(A)TGPNLHGLFGR SEQ ID NO: 18 HK_(T)TGPNLHGLFGR SEQ ID NO: 19 KTGQAPGFSYTDANK SEQ ID NO: 20 K_(DN)TGQAPGFSYTDANK SEQ ID NO: 21 K_(A)TGQAPGFSYTDANK SEQ ID NO: 22 K_(T)TGQAPGFSYTDANK SEQ ID NO: 23 GGKHKTGPNLHGLFGR SEQ ID NO: 24 GGK*HK*TGPNLHGLFGR SEQ ID NO: 25 GGK_(A)HK_(T)TGPNLHGLFGR SEQ ID NO: 26 GGK_(T)HK_(A)TGPNLHGLFGR SEQ ID NO: 27 NKPELYQIDYLGTK SEQ ID NO: 28 NK_(A)PELYQIDYLGTK SEQ ID NO: 29 LGSQSLGVSNKFEK SEQ ID NO: 30 LGSQSLGVSNK_(T)FEK SEQ ID NO: 31 GDVEKGK SEQ ID NO: 32 Ac-GDVEKGK SEQ ID NO: 33 Ac-GDVEK_(T)GK SEQ ID NO: 34 Ac-GDVEK_(A)GK SEQ ID NO: 35 KIFVQK SEQ ID NO: 36 K_(A)IFVQK SEQ ID NO: 37 K_(T)IFVQK SEQ ID NO: 38 KGER SEQ ID NO: 39 EDLIAYLKK SEQ ID NO: 40 EDLIAYLK_(A)K SEQ ID NO: 41 EDLIAYLK_(T)K SEQ ID NO: 42 KATNE SEQ ID NO: 43 K_(A)ATNE SEQ ID NO: 44 GGKHK SEQ ID NO: 45 GGK_(T)HK SEQ ID NO: 46 TGQAPGFSYTDANKNK SEQ ID NO: 47 TGQAPGFSYTDANK_(T)NK SEQ ID NO: 48 YIPGTKMIFAGIK SEQ ID NO: 49 YIPGTKM_(OX)IFAGIK SEQ ID NO: 50 YIPGTK_(A)M_(OX)IFAGIK SEQ ID NO: 51 KYIPGTK SEQ ID NO: 52 K_(T)YIPGTK SEQ ID NO: 53 MIFAGIKK SEQ ID NO: 54 M_(OX)IFAGIKK SEQ ID NO: 55 M_(OX)IFAGIK_(T)K SEQ ID NO: 56 MIFAGIK_(T)K SEQ ID NO: 57 TLTGKTITLEVEPSDTIENVK SEQ ID NO: 58 IQDKEGIPPDQQR SEQ ID NO: 59 IQDK_(A)EGIPPDQQR SEQ ID NO: 60 LIFAGKQLEDGR SEQ ID NO: 61 LIFAGK_(A)QLEDGR SEQ ID NO: 62 LIFAGK_(T)QLEDGR SEQ ID NO: 63 LIFAGK⁴⁸QLEDGR SEQ ID NO: 64 TLSDYNIQKESTLHLVLR SEQ ID NO: 65 TLSDYNIQK_(T)ESTLHLVLR SEQ ID NO: 66 ATATGPKQQEITTNLENHFK SEQ ID NO: 67 ATATGPK_(A)QQEITTNLENHFK SEQ ID NO: 68 KVPDK SEQ ID NO: 69 K_(T)VPDK SEQ ID NO: 70 KVAHTSYK SEQ ID NO: 71 K_(T)VAHTSYK SEQ ID NO: 72 VLVDKSR SEQ ID NO: 73 VLVDK_(A)SR SEQ ID NO: 74 IFKPQEIK SEQ ID NO: 75 IFK_(T)PQEIK SEQ ID NO: 76 LYKLNDK SEQ ID NO: 77 LYK_(A)LNDK SEQ ID NO: 78 IHAQNYLKTYNEDIPVEILVR SEQ ID NO: 79 IHAQNYLK_(T)TYNEDIPVEILVR SEQ ID NO: 80 YKTNLYK SEQ ID NO: 81 YK_(A)TNLYK SEQ ID NO: 82 YK_(T)TNLYK SEQ ID NO: 83 EFLEKNYDR SEQ ID NO: 84 EFLEK_(A)NYDR SEQ ID NO: 85 NSKTVR SEQ ID NO: 86 NSK_(Ak)TVR SEQ ID NO: 87 ILKQVMEEK SEQ ID NO: 88 ILK_(T)QVMEEK SEQ ID NO: 89 ELKEK SEQ ID NO: 90 SYKFPR SEQ ID NO: 91 SYK_(A)FPR SEQ ID NO: 92 EEKQK SEQ ID NO: 93 EEK_(T)QK SEQ ID NO: 94 LKEER SEQ ID NO: 95 LK_(A)EER SEQ ID NO: 96 YLKMR SEQ ID NO: 97 YLKM_(OX)R SEQ ID NO: 98 YLK_(A)M_(OX)R SEQ ID NO: 99 VQDSVILASSKAVTR SEQ ID NO: 100 VQDSVILASSK_(Ak)AVTR SEQ ID NO: 101 GISVLKDSDDKTR SEQ ID NO: 102 GISVLK_(T)DSDDKTR SEQ ID NO: 103 FKNSVK SEQ ID NO: 104 FK_(A)NSVK SEQ ID NO: 105 KLAVER SEQ ID NO: 106 NQYEPGTNGKVK SEQ ID NO: 107 NQYEPGTNGK_(A)VK SEQ ID NO: 108 KPLK SEQ ID NO: 109 AELEKLVDHHPEGLSAR SEQ ID NO: 110 AELEK_(DN)LVDHHPEGLSAR SEQ ID NO: 111 AELEK_(A)LVDHHPEGLSAR SEQ ID NO: 112 AELEK_(T)LVDHHPEGLSAR SEQ ID NO: 113 KYIPGTKMIFAGIK SEQ ID NO: 114 KYIPGTKMoxIFAGIK SEQ ID NO: 115 KYIPGTKMIFAGIKK SEQ ID NO: 116 KYIPGTKMoxIFAGIKK SEQ ID NO: 117 MIFAGIKKK SEQ ID NO: 118 MoxIFAGIKKK SEQ ID NO: 119 EDLIAYLKKATNE SEQ ID NO: 120 YIPGTKMIFAGIKKK SEQ ID NO: 121 YIPGTKMoxIFAGIKKK SEQ ID NO: 122 MIFAGIKKKGER SEQ ID NO: 123 MoxIFAGIKKKGER SEQ ID NO: 124 GKKIFVQK SEQ ID NO: 125 GDVEKGKKIFVQK SEQ ID NO: 126 Ac-GDVEKGKKIFVQK SEQ ID NO: 127 MQIFVKTLTGK SEQ ID NO: 128 AKIQDK SEQ ID NO: 129 LIFAGKQLEDGRTLSDYNIQK SEQ ID NO: 130 AKIQDKEGIPPDQQR SEQ ID NO: 131 AKAEAAEFR SEQ ID NO: 132 TFLEKR SEQ ID NO: 133 KVTSTLLEQDTSTEK SEQ ID NO: 134 STLKLQDTR SEQ ID NO: 135 ITPSKVSK SEQ ID NO: 136 ILIEKAR SEQ ID NO: 137 TAELIKELK SEQ ID NO: 138 LLVPQKNVK SEQ ID NO: 139 EAVKQAAK SEQ ID NO: 140 TNLYKLK SEQ ID NO: 141 QELAKSIR SEQ ID NO: 142 IVDKDGIR SEQ ID NO: 143 KLSINSAAR SEQ ID NO: 144 KEFYELK Ac—Acetyl Xaa_(A)—Alkene modification Xaa_(Ak)—Alkane modification Xaa_(DN)—Dead-end modification Xaa_(T)—Thiol modification Xaa_(S)—Sulfenic acid modification Xaa_(OX)—Oxidation *Intra-peptide linkage Xaa⁴⁸—Inter-peptide linkage

TABLE 7 K-K Linkage MS^(n) m/z z Sequence Modification(s) K6-K9 MS2 615.3107 3 MS3 828.41 1 MGDVEK_(A)GK (SEQ Met-loss + Acetyl@1; Akene@6 ID NO: 145) MS3 408.75 2 K_(A)IFVQK (SEQ ID NO: Alkene@9 36) K6-K88 MS2 457.4806 4 MS3 478.76 2 MGDVEK_(A)GKK (SEQ Met-loss + Acetyl@1, Alkene@6 ID NO: 146) MS3 336.20 2 K_(A)KGER (SEQ ID NO: AlKene@88 15) K6-K89 MS2 555.2882 5 MS3 478.76 2 MGDVEK_(A)GKK (SEQ Met-loss + Acetyl@1, Alkene@6 ID NO: 146) MS3 539.64 3 KK_(A)GEREDLIAYLK Alkene@89 (SEQ ID NO: 147) K8I9-K88* MS2 482.2605 4 MS3 528.32 2 GK_(A)K_(A)IEVQK (SEQ ID Alkene@8, Alkene@9 NO: 148) MS3 336.20 2 K_(A)KGER (SEQ ID NO: Alkene@88 15) K9-K88 MS2 422.4780 4 MS3 408.75 2 K_(A)IFVQK (SEQ ID NO: Alkene@9 36) MS3 336.20 2 K_(A)KGER (SEQ ID NO: Alkene@88 15) K9-K88I89** MS2 527.2882 5 MS3 408.75 2 K_(A)IFTVQK (SEQ ID NO: Alkene@9 36) MS3 600.31 3 K_(T)KGEREDLIAYLK ThiolB@88I89 (SEQ ID NO: 149) Or KK_(T)GEREDLIAYLK (SEQ ID NO: 150) K87-K89 MS2 530.6801 5 MS3 481.28 MIFAGIK_(A)K (SEQ ID Alkene@87 NO: 151) MS3 496.94 3 K_(A)GEREDLIAYLK Alkene@89 (SEQ ID NO: 152) Note: K_(A): aikene modified lysine; K_(T): unsaturated thiol modified lysine. *Either K8 or K9 was inter-linked with K88. **Either K88 or K89 was inter-linked with K9. ThiolB is the thiol fragment β_(t) shown in the workflow in FIG. 20.

TABLE 8 1) Click Reaction On Protein 2) Click Reaction Alkene, 1B) Cell On Peptide 1A) Cell Lysate Fractionation 2) Ultrafiltration Sulfenic or Best Best Best Thiol Gene Num Expect Num Expect Num Expect Modified Acc# Name Unique % Cov Val Unique % Cov Val Unique % Cov Val peptide O60814 H2B1K 38 79.4 2.00E−10 24 81 7.00E−10 19 70.6 2.50E−09 Yes P06733 ENOA 56 90.6 5.50E−09 3 6.2 8.80E−05 8 17.7 2.20E−05 Yes P06748 NPM 29 59.9 1.90E−09 23 38.8 7.20E−07 2 7.1 6.60E−05 Yes P06899 H2B1J 38 79.4 2.00E−10 23 79.4 7.00E−10 17 70.6 2.50E−09 Yes P07197 NFM 75 60.9 2.80E−08 90 51.6 8.10E−10 6 4.4 3.20E−04 Yes P07900 HS90A 38 49 5.50E−09 10 15 1.90E−07 5 5.3 5.60E−06 Yes P07910 HNRPC 19 43.8 4.80E−07 5 8.5 2.20E−04 8 19.9 3.60E−04 Yes P08107 HSP71 69 71.8 2.80E−09 10 16.4 3.50E−09 17 31.4 1.00E−06 Yes P08238 HS90B 41 57.9 5.50E−09 7 9.1 3.30E−07 5 5.4 5.60E−06 Yes P08670 VIME 40 74.5 5.10E−08 24 34.3 9.40E−08 1 2.1 0.0022 Yes P0C0S5 H2AZ 6 33.6 3.80E−05 4 25.8 7.10E−06 3 23.4 3.20E−04 Yes P0C0S8 H2A1 24 82.3 2.90E−09 11 48.5 1.20E−07 13 55.4 2.00E−07 Yes P10412 H14 41 71.2 7.00E−09 15 39.7 1.20E−06 15 42 1.10E−05 Yes P10809 CH60 39 66.1 1.40E−08 2 3.3 2.80E−04 5 9.9 4.50E−05 Yes P12277 KCRB 17 54.1 2.70E−07 3 5 2.30E−05 3 5 1.50E−04 Yes P13639 EF2 55 55.4 1.50E−07 4 5.2 0.0014 6 7 0.0012 Yes P14314 GLU2B 5 10.2 7.10E−05 Yes P16403 H12 37 70.4 7.00E−09 14 35.7 1.20E−06 18 50.2 7.50E−06 Yes P19338 NUCL 27 32.7 8.40E−08 14 18.2 1.70E−05 Yes P20671 H2A1D 25 82.3 2.90E−09 11 48.5 1.20E−07 13 55.4 2.00E−07 Yes P20700 LMNB1 11 18.1 1.70E−05 11 15.5 1.20E−05 Yes P23527 H2B1O 38 79.4 2.00E−10 21 79.4 7.00E−10 17 70.6 2.50E−09 Yes P24534 EF1B 5 28.4 4.20E−08 1 3.1 8.10E−04 Yes P27824 CALX 13 21.1 9.60E−07 1 2.7 2.00E−05 1 1.7 1.40E−04 Yes P30101 PDIA3 11 24.8 8.70E−06 2 2.2 1.80E−05 Yes P51572 BAP31 3 11.8 1.70E−04 2 8.1 9.80E−05 Yes P52272 HNRPM 25 41.2 2.50E−09 4 5.2 1.50E−06 Yes P61353 RL27 5 24.3 7.90E−07 2 29.4 6.80E−04 Yes P61604 CH10 8 65.7 1.60E−09 2 11.8 1.70E−07 2 11.8 2.30E−07 Yes P61978 HNRPK 29 52.9 2.90E−08 4 13.8 6.40E−10 2 6.3 7.90E−05 Yes P62805 H4 29 82.5 2.00E−07 19 71.8 7.60E−08 18 75.7 1.60E−06 Yes P62807 H2B1C 38 79.4 2.00E−10 24 81 7.00E−10 20 70.6 2.50E−09 Yes P62826 RAN 10 37.5 2.90E−06 6 28.2 4.60E−07 Yes P62841 RS15 4 26.9 1.20E−07 2 13.8 3.20E−04 Yes P62937 PPIA 24 92.7 1.20E−08 2 13.3 7.60E−06 3 29.7 5.00E−06 Yes Q00839 HNRPU 20 22.9 1.10E−05 12 10.1 3.30E−09 3 4.6 9.20E−06 Yes Q02878 RL6 14 46.2 3.10E−07 4 16.7 1.60E−05 Yes Q14103 HNRPD 9 18 5.00E−08 3 9.6 2.40E−06 2 5.1 5.10E−05 Yes Q15149 PLEC 25 5.7 2.10E−07 Yes Q15233 NONO 19 44.4 1.70E−07 12 17.4 3.10E−06 2 4 1.30E−04 Yes Q16778 H2B2E 38 79.4 2.00E−10 23 79.4 7.00E−10 18 70.6 2.50E−09 Yes Q6FI13 H2A2A 24 82.3 2.90E−09 11 48.5 1.20E−07 13 55.4 2.00E−07 Yes Q71DI3 H32 24 60.3 2.20E−06 20 56.6 2.50E−05 15 58.1 6.90E−06 Yes Q93079 H2B1H 38 79.4 2.00E−10 22 81 7.00E−10 19 70.6 2.50E−09 Yes Q9NVA2 SEPT11 3 7 0.0017 Yes A2RU54 HMX2 2 2.9 3.30E−04 Yes O00148 DX39A 9 21.3 1.60E−06 1 3.5 1.40E−05 Yes O00231 PSD11 4 11.4 2.10E−04 Yes O00232 PSD12 4 9 1.30E−04 2 9.2 1.60E−05 Yes O00264 PGRC1 2 11.8 1.30E−09 Yes O00410 IPO5 6 5.7 3.00E−04 Yes O00425 IF2B3 3 6.7 9.10E−06 Yes O00567 NOP56 6 12.5 2.40E−04 1 1.9 4.40E−05 Yes O00571 DDX3X 16 26.6 2.70E−07 1 2.4 1.60E−04 Yes O14737 PDCD5 2 19.2 3.90E−04 Yes O14979 HNRDL 7 17.9 6.20E−08 1 2.4 5.10E−05 Yes O14980 XPO1 11 12 6.80E−06 Yes O15042 SR140 1 0.8 0.0014 1 1.4 3.10E−05 Yes O15260 SURF4 4 23 5.50E−06 1 8.9 2.10E−04 Yes O15347 HMGB3 3 19 1.00E−06 Yes O15371 EIF3D 3 5.3 6.00E−04 Yes O15372 EIF3H 2 8.2 7.00E−05 Yes O15397 IPO8 3 3.2 3.10E−06 Yes O15511 ARPC5 2 14.6 2.00E−05 Yes O15523 DDX3Y 11 17.9 9.10E−06 1 2.4 1.60E−04 Yes O43169 CYB5B 2 17.1 1.60E−05 Yes O43175 SERA 10 22.7 1.20E−06 Yes O43390 HNRPR 10 17.5 5.00E−06 Yes O43707 ACTN4 8 9.4 3.60E−04 1 1 0.0015 Yes O43776 SYNC 4 8.4 2.30E−06 Yes O60264 SMCA5 6 5.6 2.20E−05 Yes O60506 HNRPQ 10 17.5 5.00E−06 Yes O60841 IF2P 4 3.5 1.70E−04 Yes O75131 CPNE3 3 5 1.50E−04 Yes O75347 TBCA 2 17.6 5.20E−04 Yes O75367 H2AY 5 20.7 1.00E−06 1 5.6 0.0037 Yes O75369 FLNB 2 1.1 6.00E−05 Yes O75390 CISY 7 15 8.10E−06 Yes O75396 SC22B 3 16.3 8.30E−04 Yes O75436 VP26A 2 6.1 7.10E−05 Yes O75475 PSIP1 3 7.9 7.10E−05 Yes O75533 SF3B1 5 4.6 6.50E−07 Yes O75534 CSDE1 3 4.4 1.80E−04 Yes O75643 U520 15 8 6.60E−07 Yes O75821 EIF3G 3 12.2 1.10E−04 Yes O75844 FACE1 3 8.4 1.00E−04 Yes O76021 RL1D1 7 15.3 6.40E−06 4 5.9 1.30E−04 Yes O94826 TOM70 3 5.1 1.10E−04 Yes O95202 LETM1 3 4.5 9.50E−06 Yes O95232 LC7L3 2 6.9 1.60E−06 Yes O95373 IPO7 4 5 6.30E−05 Yes O95433 AHSA1 2 5.9 6.10E−04 Yes O95757 H574L 4 6.2 1.80E−06 Yes O95782 AP2A1 4 5.1 1.60E−05 Yes O95831 AIFM1 6 12.7 3.30E−04 Yes P00387 NB5R3 4 16.9 1.60E−06 Yes P00441 SODC 3 25.3 3.50E−06 Yes P00491 PNPH 4 18.7 2.10E−05 Yes P00492 HPRT 6 34.9 1.10E−06 Yes P00558 PGK1 16 38.8 1.30E−06 Yes P00918 CAH2 9 43.8 2.20E−07 Yes P01893 HLAH 1 3.9 0.0038 1 3 6.10E−04 Yes P02545 LMNA 4 6.5 1.50E−04 3 3 0.005 Yes P04075 ALDOA 13 31.9 1.50E−08 Yes P04264 K2C1 7 12.9 1.10E−04 2 3.3 1.30E−05 Yes P04350 TBB4A 27 58.1 2.10E−07 2 5.2 0.0037 Yes P04406 G3P 29 69.9 1.20E−09 4 16.7 6.30E−05 4 14.3 1.60E−05 Yes P04908 H2A1B 23 82.3 2.90E−09 11 48.5 1.20E−07 12 52.3 2.00E−07 Yes P05023 AT1A1 13 15.4 9.00E−07 Yes P05091 ALDH2 2 4.3 3.50E−04 Yes P05141 ADT2 22 49.3 2.50E−08 7 32.6 1.30E−09 3 8.1 1.70E−05 Yes P05198 IF2A 5 16.8 2.00E−05 Yes P05204 HMGN2 4 40 2.60E−06 Yes P05387 RLA2 5 70.4 1.30E−06 1 14.8 3.10E−06 2 25.2 2.40E−04 Yes P05388 RLA0 9 28.7 2.60E−07 Yes P05455 LA 8 22.8 4.50E−06 Yes P05783 K1C18 3 6.3 4.60E−04 Yes P06454 PTMA 6 37.8 8.60E−07 2 29.7 8.20E−05 Yes P06576 ATPB 18 41.4 1.40E−07 1 4.7 5.10E−04 Yes P06732 KCRM 2 2.9 4.70E−06 1 3.7 4.70E−04 Yes P07195 LDHB 13 45.8 2.50E−08 3 12 1.10E−07 Yes P07196 NFL 29 48.3 3.60E−09 18 23.9 9.40E−08 Yes P07237 PDIA1 12 26 4.80E−06 Yes P07339 CATD 2 4.6 5.60E−06 Yes P07437 TBB5 37 75.7 7.80E−08 2 5.2 0.0037 Yes P07477 TRY1 5 7.3 2.90E−04 2 7.3 0.0019 Yes P07602 SAP 3 7.1 9.00E−05 Yes P07737 PROF1 14 85 2.40E−08 1 7.9 0.0015 Yes P07814 SYEP 6 4.1 2.70E−07 Yes P08133 ANXA6 9 14.1 1.90E−04 Yes P08195 4F2 4 8.3 1.90E−05 2 5.2 0.0018 Yes P08243 ASNS 3 6.1 2.00E−05 Yes P08559 ODPA 2 5.1 1.80E−04 Yes P08621 RU17 5 9.8 9.10E−04 Yes P09429 HMGB1 9 31.2 1.00E−06 2 13.5 7.00E−05 2 6.5 1.80E−05 Yes P09622 DLDH 4 8.8 2.20E−05 Yes P09651 ROA1 14 38.2 2.10E−10 6 16.4 1.20E−07 5 13.7 2.70E−05 Yes P09874 PARP1 24 27.9 4.00E−08 3 3.9 7.20E−06 2 3 4.40E−04 Yes P0C7M2 RA1L3 11 33.8 1.30E−07 4 14.1 6.90E−07 3 10.9 9.60E−04 Yes P0CG48 UBC 19 9.6 8.20E−07 9 6 2.80E−08 9 8.3 4.20E−06 Yes P10599 THIO 7 41.9 8.20E−06 1 12.4 0.0014 Yes P11021 GRP78 23 42.2 3.90E−08 1 1.7 8.30E−04 Yes P11142 HSP7C 33 37.8 2.90E−08 4 8.4 1.50E−04 3 5.9 3.20E−05 Yes P11387 TOP1 3 3.5 7.30E−04 Yes P11388 TOP2A 7 5.8 8.40E−06 Yes P11586 C1TC 14 18.3 3.80E−07 Yes P11940 PABP1 15 29.7 3.30E−09 Yes P12004 PCNA 10 31 8.50E−07 Yes P12081 SYNC 6 12.2 9.90E−05 Yes P12235 ADT1 13 33.2 3.20E−07 2 12.8 1.50E−04 2 4 1.70E−05 Yes P12236 ADT3 17 39.9 3.20E−07 5 32.6 1.50E−05 2 4 1.70E−05 Yes P12268 IMDH2 6 14.8 1.20E−07 Yes P12270 TPR 1 0.4 0.0013 2 1.3 6.90E−05 Yes P12814 ACTN1 8 10 3.60E−04 1 1 0.0015 Yes P12956 XRCC6 14 29.6 8.80E−08 1 1.6 0.0026 Yes P13010 XRCC5 22 38.7 1.20E−06 2 3.8 1.40E−05 Yes P13667 PDIA4 18 34.3 3.90E−07 1 1.6 5.90E−04 Yes P13796 PLSL 10 20.6 4.20E−05 Yes P13861 KAP2 3 12.9 9.50E−06 Yes P14618 KPYM 23 51.2 1.50E−08 2 4.1 9.20E−05 Yes P14625 ENPL 23 27.3 2.00E−07 1 1.7 1.50E−04 2 0.9 8.10E−04 Yes P14678 RSMB 6 17.5 1.90E−06 1 4.6 4.70E−05 Yes P14866 HNRPL 18 35.8 2.20E−07 4 13.4 1.20E−05 1 1.9 6.30E−05 Yes P15170 ERF3A 4 5.2 7.00E−05 Yes P15311 EZRI 5 7.5 1.20E−05 Yes P15374 UCHL3 2 8.7 0.0011 Yes P15880 RS2 10 37.5 4.10E−06 1 3.8 9.30E−05 Yes P16104 H2AX 12 67.8 1.40E−08 5 42.7 3.40E−07 4 21 3.00E−04 Yes P16152 CBR1 6 25.6 1.20E−06 Yes P16402 H13 27 48.4 7.00E−09 11 23.5 1.20E−06 12 28.5 1.10E−05 Yes P16949 STMN1 2 12.1 2.60E−04 Yes P16989 DBPA 6 15.1 3.10E−06 Yes P17066 HSP76 19 17.9 2.80E−09 3 3.1 2.30E−05 5 9.5 1.70E−06 Yes P17661 DESM 5 6.4 1.40E−04 4 4.7 5.70E−06 Yes P17844 DDX5 16 27.4 6.00E−07 1 1.6 1.60E−04 Yes P18077 RL35A 3 27.3 7.80E−05 1 12.7 3.60E−06 Yes P18124 RL7 10 40.7 1.30E−05 Yes P18621 RL17 4 20.7 1.00E−04 2 14.1 6.90E−04 Yes P18669 PGAM1 11 52 5.10E−08 Yes P18754 RCC1 3 7.8 6.30E−06 Yes P19367 HXK1 3 3.4 1.10E−06 Yes P21333 FLNA 5 2.3 6.00E−05 1 0.5 2.70E−05 Yes P21796 VDAC1 8 35 4.40E−07 Yes P21912 DHSB 2 7.5 2.40E−05 Yes P22234 PUR6 10 23.3 5.00E−08 Yes P22307 NLTP 6 9.7 3.20E−04 Yes P22314 UBA1 22 26.1 2.50E−07 Yes P22392 NDKB 6 48 4.90E−05 1 7.9 7.80E−04 Yes P22626 ROA2 23 61.5 4.80E−11 8 22.9 1.70E−08 5 11.6 1.50E−04 Yes P23246 SFPQ 12 21.4 4.80E−07 1 1.8 9.10E−04 Yes P23284 PPIB 7 35.2 1.40E−05 2 12.5 4.70E−06 Yes P23396 RS3 14 60.1 8.60E−07 1 9.1 1.30E−04 1 3.7 4.20E−04 Yes P23526 SAHH 7 17.6 9.00E−08 1 3 1.40E−04 Yes P23528 COF1 9 51.8 1.30E−08 1 7.8 0.0055 Yes P23588 IF4B 2 3.9 0.0016 Yes P24539 AT5F1 6 28.9 9.70E−07 Yes P24941 CDK2 3 10.4 1.30E−04 Yes P25398 RS12 5 40.2 8.90E−08 1 6.8 5.80E−04 Yes P25705 ATPA 19 45.8 1.90E−07 5 11.8 6.50E−07 1 1.8 3.60E−04 Yes P25789 PSA4 5 20.7 4.60E−05 Yes P26038 MOES 5 6.1 1.20E−05 Yes P26358 DNMT1 3 2.4 1.10E−04 Yes P26368 U2AF2 6 13.3 8.10E−06 1 2.3 1.30E−04 Yes P26583 HMGB2 3 15.3 1.00E−06 2 13.9 1.90E−04 1 6.7 5.20E−05 Yes P26599 PTBP1 13 27.3 6.90E−09 2 6 3.40E−07 Yes P26639 SYTC 7 10.7 9.50E−05 Yes P26641 EF1G 14 32.5 1.60E−07 1 2.3 0.0027 Yes P27348 1433T 10 45.3 2.20E−08 Yes P27694 RFA1 5 10.6 5.10E−05 Yes P27695 APEX1 5 18.2 2.30E−06 Yes P27708 PYR1 7 3.5 6.80E−05 Yes P27797 CALR 16 47.2 1.30E−08 1 3.1 1.90E−05 3 6.2 5.40E−04 Yes P28066 PSA5 3 17 7.60E−05 Yes P28288 ABCD3 2 4.7 3.40E−07 Yes P28838 AMPL 4 9.8 3.30E−05 Yes P29692 EF1D 9 35.2 5.30E−06 1 2.5 8.10E−04 Yes P30040 ERP29 3 12.3 7.20E−05 Yes P30041 PRDX6 8 44.6 8.70E−10 Yes P30048 PRDX3 6 25.4 2.50E−06 2 11.7 0.0034 Yes P30050 RL12 5 24.8 1.10E−06 1 10.9 4.70E−09 Yes P30084 ECHM 5 24.8 7.70E−07 1 4.1 0.0062 Yes P30153 2AAA 6 16 5.00E−07 Yes P30520 PURA2 4 10.5 4.00E−05 Yes P30626 SORCN 3 14.6 0.0013 Yes P31040 DHSA 3 8.9 2.00E−06 Yes P31930 QCR1 2 3.8 5.00E−04 Yes P31939 PUR9 8 19.3 4.30E−07 Yes P31943 HNRH1 13 27.6 1.90E−07 2 4.7 2.50E−08 Yes P31946 1433B 9 42.3 9.00E−07 Yes P31947 1433S 3 9.3 0.0021 Yes P31948 STIP1 10 15.8 3.50E−06 Yes P32119 PRDX2 7 27.8 9.40E−06 Yes P32969 RL9 7 45.3 3.70E−07 1 5.2 3.10E−05 Yes P33778 H2B1B 31 70.6 2.00E−10 16 68.3 7.00E−10 14 58.7 2.50E−09 Yes P33992 MCM5 4 6.9 7.40E−07 Yes P34931 HS71L 30 32.6 4.90E−09 3 4.1 7.40E−04 5 8.6 3.20E−05 Yes P34932 HSP74 12 18.1 5.50E−07 Yes P35232 PHB 10 42.6 3.30E−07 2 3.7 0.0049 1 4.4 2.50E−07 Yes P35241 RADI 5 6.3 1.20E−05 Yes P35268 RL22 5 52.3 1.40E−06 2 18.8 2.20E−05 Yes P35579 MYH9 5 3.3 1.10E−06 3 1.5 1.00E−04 Yes P35580 MYH10 3 1.8 1.40E−05 2 1.1 2.70E−05 Yes P35606 COPB2 2 2.3 4.00E−04 1 1.2 1.00E−06 Yes P35659 DEK 5 16.3 1.30E−04 Yes P36542 ATPG 4 21.5 3.60E−06 Yes P36578 RL4 14 33.5 5.10E−06 Yes P36873 PP1G 7 19.5 6.20E−06 1 4.6 1.10E−09 Yes P37802 TAGL2 12 62.8 1.40E−07 1 6 5.90E−04 Yes P37837 TALDO 5 16.9 4.50E−05 Yes P38117 ETFB 5 19.2 8.80E−06 Yes P38159 RBMX 13 30.9 9.40E−07 Yes P38646 GRP75 27 41.8 5.00E−09 Yes P38919 IF4A3 7 18.5 6.40E−07 3 5.8 4.00E−08 Yes P39019 RS19 11 57.9 1.40E−06 1 7.6 6.20E−04 Yes P39023 RL3 10 30.5 2.30E−05 2 5.2 8.90E−04 Yes P39687 AN32A 4 19.7 2.20E−07 Yes P40227 TCPZ 11 26.9 8.70E−07 Yes P40429 RL13A 3 14.3 1.30E−04 Yes P40925 MDHC 5 18.3 4.10E−08 Yes P40926 MDHM 23 68.3 1.10E−09 1 2.7 2.00E−04 1 2.7 2.30E−05 Yes P40939 ECHA 7 12.7 1.80E−07 Yes P41091 IF2G 2 6.6 5.30E−06 Yes P41219 PERI 4 6.4 2.50E−06 2 4.5 4.40E−06 Yes P41250 SYG 6 12.2 2.00E−07 Yes P41252 SYIC 10 9.5 2.80E−05 Yes P42166 LAP2A 7 11.1 6.60E−07 Yes P42167 LAP2B 8 19.4 6.60E−07 3 7 8.10E−04 Yes P42285 SK2L2 2 1.9 2.80E−04 Yes P42704 LPPRC 17 15.9 8.70E−07 Yes P42766 RL35 1 8.1 1.30E−04 1 8.1 6.60E−04 Yes P43243 MATR3 13 17.9 2.00E−06 1 1.1 0.0017 Yes P43246 MSH2 3 3.7 4.00E−04 Yes P43487 RANG 3 15.4 7.30E−06 Yes P45880 VDAC2 10 28.9 2.90E−07 Yes P45973 CBX5 2 11.5 2.30E−04 Yes P46013 K167 4 1.3 7.50E−05 Yes P46087 NOP2 3 4.1 0.0037 1 1.2 1.80E−05 Yes P46776 RL27A 2 14.2 1.00E−04 1 8.8 6.20E−07 1 7.4 1.70E−04 Yes P46777 RL5 7 26.9 2.00E−07 Yes P46778 RL21 3 25 1.20E−07 1 9.4 4.40E−05 Yes P46779 RL28 7 40.1 2.80E−05 Yes P46781 RS9 12 43.8 7.00E−06 Yes P46782 RS5 8 46.1 1.10E−06 Yes P46783 RS10 2 14.5 1.60E−05 Yes P46940 IQGA1 5 4 3.70E−05 Yes P47914 RL29 3 16.4 6.20E−08 Yes P48643 TCPE 17 32.3 1.50E−07 Yes P49207 RL34 5 30.8 3.20E−04 Yes P49327 FAS 31 14.9 7.70E−07 1 0.4 0.0026 Yes P49368 TCPG 19 42.9 8.70E−07 Yes P49411 EFTU 7 18.6 2.10E−07 Yes P49419 AL7A1 2 4.6 1.10E−06 Yes P49458 SRP09 2 26.7 4.00E−05 Yes P49915 GUAA 7 13.4 7.00E−05 Yes P50454 SERPH 4 12.4 6.60E−06 Yes P50502 F10A1 4 12.2 1.30E−05 Yes P50914 RL14 9 35.3 1.10E−06 2 10.7 2.30E−06 Yes P50990 TCPQ 24 47.8 2.10E−08 Yes P50991 TCPD 20 38.4 7.50E−08 Yes P50995 ANX11 2 4.6 9.00E−05 Yes P51148 RAB5C 4 22.2 7.60E−05 Yes P51659 DHB4 4 5.7 4.50E−05 1 4.3 9.80E−05 Yes P51665 PSD7 2 11.7 0.0021 1 7.4 0.0018 Yes P51991 ROA3 7 21.4 3.70E−11 4 8.5 1.10E−07 1 3.7 0.0022 Yes P52209 6PGD 10 31.9 2.50E−07 Yes P52597 HNRPF 9 28 1.90E−07 1 2.2 3.40E−04 Yes P52701 MSH6 4 3.6 9.80E−06 Yes P52815 RM12 2 11.1 8.30E−06 Yes P52907 CAZA1 4 18.5 4.70E−06 Yes P53396 ACLY 12 14.1 1.60E−06 Yes P53618 COPB 1 1.2 2.10E−04 1 1.2 6.20E−04 Yes P53621 COPA 7 6.9 8.60E−07 Yes P53999 TCP4 2 18.9 5.10E−04 Yes P54136 SYRC 6 9.8 1.40E−04 Yes P54652 HSP72 14 15 3.90E−08 2 3.8 3.20E−05 Yes P54709 AT1B3 6 22.9 5.40E−06 Yes P55036 PSMD4 4 12.5 4.20E−07 Yes P55060 XPO2 16 23.4 4.60E−07 Yes P55072 TERA 19 31.4 6.70E−07 Yes P55084 ECHB 9 19.4 2.40E−04 Yes P55209 NP1L1 4 12.5 2.00E−06 Yes P55263 ADK 2 9.9 2.00E−07 Yes P55786 PSA 6 7.8 4.90E−05 Yes P55795 HNRH2 4 13.4 2.80E−07 2 4.7 2.50E−08 Yes P57053 H2BFS 36 71.4 2.00E−10 22 72.2 7.00E−10 19 70.6 2.50E−09 Yes P58876 H2B1D 37 79.4 2.00E−10 22 81 7.00E−10 17 65.9 2.50E−09 Yes P60709 ACTB 37 74.7 3.80E−09 17 17.9 3.20E−09 18 31.7 3.80E−06 Yes P60842 IF4A1 21 57.4 1.30E−07 1 3.9 2.50E−08 Yes P60866 RS20 2 16 3.40E−07 Yes P60900 PSA6 3 13 3.50E−05 1 7.3 3.70E−05 Yes P60981 DEST 2 16.4 1.50E−06 Yes P61077 UB2D3 1 7.5 5.90E−04 2 6.8 1.30E−04 Yes P61081 UBC12 3 18.6 6.30E−05 Yes P61088 UBE2N 3 27 1.50E−05 Yes P61163 ACTZ 2 8.8 1.40E−05 Yes P61221 ABCE1 5 11.4 8.80E−06 Yes P61224 RAP1B 4 22.3 1.70E−05 Yes P61247 RS3A 9 34.8 5.60E−05 1 4.5 0.0069 2 6.8 3.00E−04 Yes P61254 RL26 5 26.2 0.0013 1 11 0.0014 Yes P61289 PSME3 5 21.3 1.10E−05 Yes P61313 RL15 4 20.6 2.00E−07 Yes P61326 MGN 3 19.9 2.90E−04 1 5.5 8.50E−04 Yes P61769 B2MG 2 21.8 8.40E−05 Yes P61956 SUMO2 3 33.7 4.70E−06 Yes P61981 1433G 8 40.9 1.60E−07 Yes P62081 RS7 4 29.4 1.20E−06 3 13.9 1.40E−04 4 28.4 1.70E−05 Yes P62136 PP1A 9 27.3 6.20E−06 1 4.5 1.10E−09 Yes P62158 CALM 6 25.5 3.00E−06 Yes P62191 PRS4 4 11.4 1.00E−05 1 3.6 2.90E−06 Yes P62244 RS15A 5 33.1 1.20E−04 Yes P62249 RS16 5 28.8 1.60E−07 Yes P62266 RS23 5 29.4 2.00E−06 1 8.4 1.90E−05 1 7.7 1.40E−06 Yes P62277 RS13 8 37.7 9.10E−07 Yes P62280 RS11 6 29.1 6.60E−04 Yes P62314 SMD1 4 54.6 2.90E−08 1 18.5 1.40E−05 Yes P62316 SMD2 2 16.9 1.20E−05 Yes P62333 PRS10 3 9.5 3.70E−05 Yes P62424 RL7A 9 35.7 3.10E−08 4 18.8 7.50E−06 4 12 1.00E−04 Yes P62495 ERF1 8 20.4 4.10E−06 1 4.6 0.0049 Yes P62701 RS4X 11 41.4 2.10E−07 1 8.7 0.0015 3 11.8 1.60E−04 Yes P62736 ACTA 24 30.8 3.70E−08 16 18 3.20E−09 14 18.6 3.80E−06 Yes P62750 RL23A 6 32.7 3.10E−06 1 6.4 0.0018 Yes P62753 RS6 4 16.1 2.40E−05 1 4.8 7.50E−04 Yes P62829 RL23 5 40 8.10E−08 3 7.1 3.40E−05 Yes P62847 RS24 4 28.6 7.20E−07 2 19.5 8.90E−05 Yes P62851 RS25 9 44.8 1.70E−05 3 21.6 0.0011 Yes P62854 RS26 3 33.9 3.30E−06 Yes P62857 RS28 4 56.5 4.00E−04 Yes P62888 RL30 5 48.7 1.40E−05 Yes P62899 RL31 3 26.4 4.50E−08 1 11.2 9.90E−04 Yes P62906 RL10A 8 26.3 2.60E−06 2 8.8 4.50E−05 Yes P62910 RL32 4 29.6 4.20E−05 2 13.3 9.70E−04 Yes P62913 RL11 3 18.5 6.40E−07 Yes P62917 RL8 2 10.5 5.80E−06 1 4.3 1.00E−04 Yes P63010 AP2B1 3 3.4 1.10E−04 Yes P63104 1433Z 7 36.3 2.80E−08 Yes P63167 DYL1 2 24.7 6.10E−06 1 13.5 4.60E−04 Yes P63173 RL38 3 45.7 1.30E−05 Yes P63208 SKP1 3 25.2 3.60E−05 Yes P63241 IF5A1 8 70.1 2.20E−07 3 24 6.70E−04 Yes P63261 ACTG 37 74.7 5.30E−09 17 17.9 3.20E−09 18 31.7 3.80E−06 Yes P63267 ACTH 24 30.9 3.70E−08 16 18.1 3.20E−09 14 18.6 3.80E−06 Yes P67809 YBOX1 9 32.1 3.10E−06 Yes P68032 ACTC 25 33.7 3.70E−08 17 21 3.20E−09 15 21.5 3.80E−06 Yes P68104 EF1A1 30 39.8 1.40E−10 10 19.7 9.20E−09 2 4.8 2.30E−05 Yes P68133 ACTS 25 33.7 3.70E−08 17 21 3.20E−09 15 21.5 3.80E−06 Yes P68363 TBA1B 31 57 1.50E−09 6 18.2 3.40E−10 4 8.2 4.90E−06 Yes P68371 TBB4B 32 69.4 2.10E−07 2 5.2 0.0037 Yes P78347 GTF2I 4 8.8 1.10E−06 Yes P78371 TCPB 17 42.6 3.10E−08 1 6.2 0.0024 Yes P78417 GSTO1 2 7.5 6.60E−06 Yes P78527 PRKDC 32 8.5 4.80E−06 2 0.6 8.90E−07 Yes P82979 SARNP 4 18.1 2.10E−04 Yes P83731 RL24 3 19.1 2.30E−06 1 8.9 2.00E−04 2 13.4 9.30E−06 Yes P84090 ERH 6 35.6 4.50E−08 3 25 1.00E−04 Yes P84098 RL19 2 13.3 8.60E−09 1 5.1 7.50E−04 Yes P99999 CYC 4 25.7 1.60E−05 Yes Q00610 CLH1 23 16.4 4.50E−08 4 3.1 6.80E−07 Yes Q00688 FKBP3 2 9.8 1.30E−05 Yes Q01082 SPTB2 2 1.1 4.80E−05 Yes Q01105 SET 4 11.4 5.20E−06 1 3.1 0.0074 1 3.1 0.0038 Yes Q01518 CAP1 2 6.1 1.40E−05 Yes Q01813 K6PP 4 5.4 8.20E−06 Yes Q02790 FKBP4 9 20.5 4.60E−05 Yes Q02880 TOP2B 4 2.5 3.70E−05 Yes Q03252 LMNB2 4 8 1.30E−06 3 3.5 8.60E−05 Yes Q04637 IF4G1 11 7.8 1.70E−06 1 0.9 0.0032 1 0.9 2.00E−05 Yes Q04760 LGUL 4 27.2 1.50E−06 Yes Q04917 1433F 3 9.3 0.0021 Yes Q05639 EF1A2 18 22 1.40E−10 5 9.7 9.20E−09 1 2.2 1.40E−04 Yes Q06830 PRDX1 17 56.3 1.10E−06 Yes Q07021 C1QBP 9 51.4 4.40E−07 1 3.9 6.80E−04 Yes Q07065 CKAP4 5 9.5 1.10E−05 Yes Q07666 KHDR1 5 9.7 1.40E−05 Yes Q07955 SRSF1 5 25.8 6.30E−05 Yes Q08211 DHX9 28 27.2 1.00E−07 2 2.2 2.10E−04 Yes Q08945 SSRP1 6 9.9 1.00E−05 2 3.9 1.70E−04 1 1.3 0.0016 Yes Q08J23 NSUN2 2 3.9 2.90E−04 Yes Q12873 CHD3 3 1.4 2.00E−04 Yes Q12905 ILF2 9 33.6 5.50E−07 2 10 4.00E−04 Yes Q12906 ILF3 13 16.6 2.90E−07 3 2.8 5.30E−06 Yes Q12931 TRAP1 10 16.9 5.50E−07 2 3.1 4.90E−05 Yes Q13148 TADBP 5 17.9 1.40E−08 Yes Q13151 ROA0 5 23.6 2.10E−07 Yes Q13162 PRDX4 6 25.5 2.40E−06 Yes Q13185 CBX3 4 22.4 3.10E−06 Yes Q13200 PSMD2 5 6.7 3.00E−06 7 16.6 2.50E−06 Yes Q13263 TIF1B 13 22.3 2.10E−07 1 1 0.0015 Yes Q13283 G3BP1 7 21.5 1.60E−06 1 4.7 0.0072 Yes Q13310 PABP4 13 25.3 3.30E−09 Yes Q13428 TCOF 4 3 7.40E−05 Yes Q13619 CUL4A 5 10 0.0012 Yes Q13748 TBA3C 25 42 1.50E−09 5 14.7 3.40E−10 3 4.7 0.0041 Yes Q13765 NACA 5 32.6 8.40E−08 2 9.8 4.70E−04 Yes Q13813 SPTN1 3 1.2 7.40E−04 4 2.2 7.00E−09 Yes Q13838 DX39B 10 23.8 5.00E−07 2 3.7 1.30E−05 Yes Q13885 TBB2A 29 58.9 8.10E−08 1 3.1 0.0037 Yes Q14151 SAFB2 3 3.5 6.70E−06 Yes Q14152 EIF3A 12 9 2.40E−05 Yes Q14204 DYNC1 11 2.3 2.90E−04 Yes Q14498 RBM39 4 10 5.50E−05 Yes Q14568 HS902 10 20.4 1.30E−05 5 14.9 3.30E−07 1 2.6 5.60E−06 Yes Q14651 PLSI 3 5.6 3.30E−05 Yes Q14677 EPN4 1 2.1 1.40E−04 1 3.2 1.30E−05 Yes Q14683 SMC1A 2 1.5 0.0012 Yes Q14684 RRP1B 1 1.5 0.0096 1 1.1 3.60E−04 Yes Q14690 RRP5 2 0.9 0.0018 2 1.1 9.10E−06 Yes Q14739 LBR 3 5.7 1.10E−05 1 2.3 3.20E−04 Yes Q14978 NOLC1 4 5.9 1.80E−05 Yes Q14997 PSME4 2 1.6 0.0017 Yes Q15029 U5S1 11 14.6 3.60E−06 1 0.9 3.70E−04 Yes Q15056 IF4H 4 22.2 4.70E−05 Yes Q15061 WDR43 1 2.2 0.0024 1 2.2 7.60E−04 Yes Q15084 PDIA6 9 28.9 3.10E−08 Yes Q15181 IPYR 9 41.2 1.30E−09 Yes Q15185 TEBP 5 27.5 9.50E−08 1 8.1 3.30E−04 Yes Q15293 RCN1 3 12.1 4.00E−05 Yes Q15365 PCBP1 7 24.4 1.50E−06 Yes Q15366 PCBP2 7 23.8 1.50E−06 Yes Q15393 SF3B3 13 12.3 1.50E−06 Yes Q15424 SAFB1 3 3.6 3.20E−06 Yes Q15819 UB2V2 2 13.8 6.00E−04 Yes Q15843 NEDD8 2 8.6 4.10E−05 Yes Q16181 SEPT7 2 5.3 2.90E−05 Yes Q16531 DDB1 9 7.6 1.50E−04 Yes Q16777 H2A2C 19 75.2 2.90E−09 7 41.1 1.20E−07 10 48.1 2.00E−07 Yes Q16881 TRXR1 2 4.2 1.40E−04 Yes Q16891 IMMT 2 2.4 9.60E−04 Yes Q1KMD3 HNRL2 3 4 2.20E−05 1 1.2 0.0012 Yes Q32P51 RA1L2 10 26.6 1.30E−07 4 14.1 6.90E−07 3 10.9 9.60E−04 Yes Q4VCS5 AMOT 3 3.8 2.10E−04 Yes Q562R1 ACTBL 13 14.9 3.70E−08 4 6.1 5.30E−07 6 11.2 1.20E−05 Yes Q58FF3 ENPLL 4 7.3 4.00E−04 2 1.8 8.10E−04 Yes Q58FG0 HS905 4 13.2 1.90E−06 Yes Q5JQF8 PAP1M 2 10 9.00E−06 Yes Q5JTH9 RRP12 1 0.8 0.0011 2 1.4 7.40E−04 Yes Q5QNW6 H2B2F 36 77 2.00E−10 19 75.4 7.00E−10 18 63.5 2.50E−09 Yes Q5T9A4 ATD3B 4 6.3 1.90E−04 1 1.4 0.0046 Yes Q6DN03 H2B2C 9 16.6 2.10E−05 8 16.6 3.40E−06 3 10.9 4.80E−05 Yes Q6DRA6 H2B2D 9 19.5 2.10E−05 8 19.5 3.40E−06 3 12.8 4.80E−05 Yes Q6NUK1 SCMC1 2 5 1.60E−05 1 5.7 0.0022 Yes Q6P2Q9 PRP8 12 5.7 5.40E−06 Yes Q6PEY2 TBA3E 15 36.7 1.50E−09 3 12.7 3.10E−06 2 3.8 0.0041 Yes Q6UB35 C1TM 2 2.9 9.30E−06 Yes Q71U36 TBA1A 31 57 1.50E−09 6 18.2 3.40E−10 4 8.2 4.90E−06 Yes Q71UI9 H2AV 6 33.6 3.80E−05 4 25.8 7.10E−06 3 23.4 3.20E−04 Yes Q7KZF4 SND1 5 6.4 5.80E−04 1 1.2 0.0022 Yes Q7L1Q6 BZW1 3 5.7 0.0012 Yes Q7L7L0 H2A3 23 82.3 2.90E−09 11 48.5 1.20E−07 12 52.3 2.00E−07 Yes Q86SE5 RALYL 2 6.5 2.40E−04 2 6.2 0.0023 Yes Q86U42 PABP2 3 14.4 1.00E−05 Yes Q86VP6 CAND1 11 12 1.10E−06 Yes Q8IUE6 H2A2B 11 74.6 1.40E−08 4 30 3.40E−07 7 29.2 2.30E−04 Yes Q8IWX8 CHERP 2 2.8 0.0028 Yes Q8N1F7 NUP93 2 5.3 7.30E−06 Yes Q8N257 H2B3B 35 74.6 2.00E−10 20 74.6 7.00E−10 14 64.3 2.50E−09 Yes Q8NB90 SPAT5 2 2.4 4.60E−04 Yes Q8NC51 PAIRB 5 17.9 4.30E−07 Yes Q8NE71 ABCF1 4 5.1 1.10E−04 Yes Q8NEN0 ARMC2 2 1.6 0.004 Yes Q8TDN6 BRX1 1 3.1 2.30E−04 1 3.4 0.0011 Yes Q92499 DDX1 5 8.9 2.30E−08 Yes Q92598 HS105 8 10.5 1.90E−05 Yes Q92616 GCN1L 3 1.4 7.50E−05 Yes Q92688 AN32B 5 24.7 2.20E−07 Yes Q92804 RBP56 3 5.4 2.50E−05 Yes Q92841 DDX17 15 24.1 5.70E−07 1 1.4 1.60E−04 Yes Q92922 SMRC1 3 3.9 4.80E−07 Yes Q92945 FUBP2 13 15.3 1.20E−05 Yes Q93077 H2A1C 22 82.3 2.90E−09 11 48.5 1.20E−07 12 52.3 2.00E−07 Yes Q969X6 CIR1A 1 1.5 0.0023 1 1.7 2.00E−04 Yes Q96A72 MGN2 3 20.9 2.90E−04 1 5.4 8.50E−04 Yes Q96AE4 FUBP1 4 6.8 1.20E−05 1 1.9 0.0045 Yes Q96AG4 LRC59 5 20.8 7.10E−06 Yes Q96KK5 H2A1H 22 82 2.90E−09 10 47.7 1.20E−07 12 54.7 2.00E−07 Yes Q96PK6 RBM14 8 13.8 6.80E−07 Yes Q96QK1 VPS35 3 3 6.00E−04 Yes Q96QV6 H2A1A 11 47.3 2.00E−07 5 35.1 3.40E−07 7 29 2.30E−04 Yes Q99460 PSMD1 4 6.4 3.40E−05 Yes Q99497 PARK7 7 45.5 7.80E−05 Yes Q99615 DNJC7 7 17 3.00E−04 Yes Q99623 PHB2 11 43.5 7.70E−08 1 3 0.01 Yes Q99729 ROAA 7 21.7 1.60E−08 3 7.8 5.10E−05 Yes Q99798 ACON 2 2.7 0.0035 Yes Q99832 TCPH 17 35.5 6.00E−09 Yes Q99873 ANM1 3 9.1 9.30E−05 Yes Q99880 H2B1L 37 79.4 2.00E−10 21 76.2 7.00E−10 17 65.9 2.50E−09 Yes Q9BPX3 CND3 3 3.9 2.00E−04 Yes Q9BQ39 DDX50 5 7.6 6.00E−05 Yes Q9BQE3 TBA1C 31 57.7 1.50E−09 6 18.3 3.40E−10 4 8.2 4.90E−06 Yes Q9BQG0 MBB1A 6 4.9 1.20E−05 3 2.4 1.40E−06 Yes Q9BRA2 TXD17 4 17.9 9.50E−05 Yes Q9BTM1 H2AJ 16 69 2.90E−09 6 34.9 1.20E−07 7 41.9 2.00E−07 Yes Q9BTT0 AN32E 3 17.2 3.70E−05 Yes Q9BUJ2 HNRL1 2 1.9 0.0073 1 2.5 0.0049 Yes Q9BVA1 TBB2B 29 58.9 8.10E−08 1 3.1 0.0037 Yes Q9BXJ9 NAA15 3 3.2 1.30E−04 Yes Q9BXP5 SRRT 2 1.9 8.80E−05 Yes Q9BY67 CADM1 2 1.8 1.60E−04 Yes Q9BZE4 NOG1 2 3.2 1.00E−03 Yes Q9BZZ5 API5 6 14.1 3.10E−07 Yes Q9GZT3 SLIRP 3 33 1.60E−04 Yes Q9H2U2 IPYR2 2 7.5 6.50E−07 Yes Q9H307 PININ 2 3.1 3.60E−05 Yes Q9H3K2 GHITM 2 6.1 6.50E−04 Yes Q9HAV4 XPO5 3 3.9 2.00E−05 Yes Q9HB71 CYBP 8 31.6 6.40E−05 Yes Q9NQ88 TIGAR 2 6.7 1.20E−04 Yes Q9NQC3 RTN4 2 2.2 1.80E−04 Yes Q9NR30 DDX21 18 30.1 8.90E−07 3 3.4 4.40E−07 Yes Q9NR31 SAR1A 2 11.6 1.30E−04 1 6.6 8.30E−04 Yes Q9NTK5 OLA1 3 9.8 2.30E−05 Yes Q9NV96 CC50A 1 3.3 1.50E−05 1 3.3 6.70E−04 Yes Q9NVI7 ATD3A 7 11.8 4.90E−06 1 1.4 0.0046 Yes Q9NVP1 DDX18 5 10 1.40E−04 1 1.5 3.30E−04 Yes Q9NX63 CHCH3 2 11.5 1.20E−05 Yes Q9NY65 TBA8 16 29.2 1.80E−08 4 9.4 3.40E−10 2 2.4 0.0041 Yes Q9NZ01 TECR 2 6.8 4.20E−04 1 4.5 1.10E−05 Yes Q9NZI8 IF2B1 9 21.1 8.60E−06 Yes Q9P258 RCC2 5 7.3 9.60E−07 Yes Q9P2J5 SYLC 10 9.7 1.40E−05 Yes Q9UHB9 SRP68 2 3.8 0.0025 Yes Q9UJS0 CMC2 2 4.6 1.10E−04 Yes Q9ULV4 COR1C 3 5.9 1.40E−04 Yes Q9UMS4 PRP19 4 11.1 1.60E−04 1 3.2 9.60E−06 Yes Q9UQ35 SRRM2 5 2.3 4.30E−06 Yes Q9UQ80 PA2G4 17 44.9 9.50E−06 Yes Q9Y262 EIF3L 6 9.6 5.60E−05 Yes Q9Y265 RUVB1 7 19.1 3.20E−06 Yes Q9Y266 NUDC 7 23 2.70E−06 Yes Q9Y277 VDAC3 3 12 4.00E−05 Yes Q9Y2L1 RRP44 3 3.5 3.00E−04 Yes Q9Y2W1 TR150 3 3.5 3.30E−05 Yes Q9Y2X3 NOP58 6 15.3 2.10E−06 1 2.8 3.60E−04 Yes Q9Y383 LC7L2 6 13.3 9.00E−06 Yes Q9Y3B4 PM14 2 20.8 1.70E−06 Yes Q9Y3F4 STRAP 4 16.9 3.90E−08 Yes Q9Y3I0 RTCB 7 14.3 1.50E−05 2 4.4 0.0042 Yes Q9Y3T9 NOC2L 2 2.7 0.0045 Yes Q9Y3U8 RL36 5 41 7.00E−06 Yes Q9Y490 TLN1 3 1.4 5.30E−06 Yes Q9Y4L1 HYOU1 3 3.3 4.90E−05 Yes Q9Y5B9 SP16H 4 3.9 1.90E−06 Yes Q9Y617 SERC 3 8.1 1.20E−04 Yes O00151 PDLI1 3 13.1 4.40E−05 O00303 EIF3F 6 20.4 3.80E−07 O00506 STK25 2 5.2 0.0011 O14579 COPE 2 9.1 2.20E−04 O14654 IRS4 5 3.9 9.10E−05 O14744 ANM5 5 8 2.10E−05 O14818 PSA7 3 16.1 5.10E−07 O14874 BCKD 2 6.8 1.80E−06 O15067 PUR4 6 5.5 6.70E−05 O15131 IMA5 3 8.6 9.30E−05 O15145 ARPC3 2 13.5 3.10E−04 O15173 PGRC2 2 10.3 1.90E−07 O15355 PPM1G 3 6.2 2.80E−07 O15382 BCAT2 2 5.1 0.0013 O43143 DHX15 6 8.7 9.90E−05 O43242 PSMD3 4 9.2 4.00E−06 O43423 AN32C 2 8.5 0.0013 O43615 TIM44 4 9.7 6.30E−04 O43684 BUB3 3 10.7 2.70E−05 O43747 AP1G1 2 2.2 0.0018 O43809 CPSF5 4 27.8 4.40E−06 O43852 CALU 2 7.6 3.40E−06 O60701 UGDH 2 3.8 0.0013 O75083 WDR1 2 2.8 0.0012 O75153 CLU 2 1.7 0.0018 O75400 PR40A 2 1.9 0.0075 O75489 NDUS3 2 9.5 1.70E−05 1 6.8 0.0012 O75494 SRS10 2 10.7 1.20E−06 O75694 NU155 2 1.2 6.10E−04 O75794 CD123 2 6.5 1.00E−04 O75947 ATP5H 5 41 3.80E−08 O75964 ATP5L 2 19.4 1.20E−05 O76003 GLRX3 5 17.6 4.00E−05 O94808 GFPT2 2 4.4 0.0012 O95486 SC24A 2 1.8 2.60E−04 O95716 RAB3D 2 11.9 9.40E−05 O95747 OXSR1 2 3 0.0023 O95861 BPNT1 2 8.4 1.20E−05 P00338 LDHA 15 53.3 8.30E−09 1 4.2 2.20E−04 P00367 DHE3 6 11.5 2.80E−05 P00374 DYR 2 18.2 0.0012 P00403 COX2 4 24.7 5.30E−06 P00505 AATM 9 21.4 4.60E−07 P00568 KAD1 2 13.4 2.30E−04 P02768 ALBU 3 5.7 2.70E−07 P02786 TFR1 2 3.4 6.00E−04 P04181 OAT 9 33 4.70E−06 1 3.6 0.0015 P04843 RPN1 9 19.1 2.20E−04 P04844 RPN2 4 9.5 1.20E−07 P06280 AGAL 2 4.9 3.30E−05 P06493 CDK1 4 18.5 7.50E−05 P06744 G6PI 10 23.3 2.50E−07 P07355 ANXA2 7 24.8 5.70E−05 1 2.4 0.008 P07741 APT 6 42.2 2.10E−05 P08134 RHOC 4 26.4 3.60E−05 P08579 RU2B 3 11.6 0.0021 1 8.9 8.50E−04 P08708 RS17 3 40 9.70E−09 P08758 ANXA5 8 25.9 4.50E−06 P08865 RSSA 8 34.9 4.70E−08 P09012 SNRPA 3 8.9 8.60E−04 P09211 GSTP1 8 41.9 3.40E−08 P09661 RU2A 3 12.5 1.30E−04 P09936 UCHL1 3 11.7 6.90E−04 P09960 LKHA4 7 16.2 1.10E−06 1 2.8 2.30E−04 P10515 ODP2 2 4.9 3.90E−06 P10768 ESTD 2 9.6 4.00E−06 P11166 GTR1 2 3.7 5.90E−04 P11177 ODPB 6 22 2.60E−06 P11802 CDK4 2 7.6 0.0037 P12955 PEPD 2 5.5 7.20E−06 P13073 COX41 4 24.9 1.40E−05 P13489 RINI 2 4.6 1.50E−05 P13645 K1C10 2 6 9.10E−06 P13797 PLST 16 29.2 1.80E−06 P13804 ETFA 7 30.3 3.20E−09 P14136 GFAP 1 1.9 4.30E−04 1 2.5 1.30E−05 P14174 MIF 4 18.3 5.20E−06 1 10.4 1.00E−04 P14406 CX7A2 2 27.7 9.90E−05 P14868 SYDC 4 7.8 1.70E−04 P14927 QCR7 2 20.7 1.40E−04 P15531 NDKA 5 38.2 5.50E−05 1 7.9 7.80E−04 P16615 AT2A2 6 6.1 1.00E−05 P17174 AATC 3 12.6 5.40E−06 P17812 PYRG1 8 17.1 4.80E−08 P17858 K6PL 2 3.1 4.00E−04 P17980 PRS6A 8 22.1 5.60E−06 P17987 TCPA 17 36.9 2.90E−06 P18085 ARF4 3 27.8 7.20E−06 1 11.1 0.0015 P18206 VINC 9 9.2 2.70E−05 P19105 ML12A 3 22.8 1.80E−06 P19623 SPEE 3 11.3 1.40E−05 P20042 IF2B 5 16.8 2.30E−05 P20336 RAB3A 2 11.8 9.40E−05 P20337 RAB3B 2 11.9 9.40E−05 P20618 PSB1 2 13.3 1.30E−07 P20674 COX5A 2 16 8.00E−04 P21266 GSTM3 3 19.6 5.10E−05 P22061 PIMT 4 21.1 1.80E−07 P22102 PUR2 8 9.2 2.20E−06 P22695 QCR2 4 8.8 1.20E−05 P23368 MAOM 3 6.8 1.20E−04 P23921 RIR1 3 5.9 0.0023 P24666 PPAC 2 15.2 4.10E−05 P24752 THIL 4 12.9 5.50E−06 P25205 MCM3 11 15.3 1.60E−05 P25786 PSA1 4 18.3 3.20E−04 P25787 PSA2 2 12 4.10E−04 P25788 PSA3 3 12.2 7.10E−05 P26373 RL13 4 19.4 8.00E−05 1 5.2 0.0012 P26640 SYVC 3 3.4 3.70E−06 P27635 RL10 4 21.5 2.10E−05 P28070 PSB4 2 12.9 1.10E−04 P28072 PSB6 3 13 3.30E−05 P28074 PSB5 5 16 3.00E−05 P28331 NDUS1 2 2.9 1.20E−04 P29401 TKT 10 23.9 4.70E−07 P30046 DOPD 2 19.5 5.10E−05 P30085 KCY 2 13.8 2.90E−06 P30086 PEBP1 3 19.3 3.20E−05 P30837 AL1B1 3 7 1.40E−04 P31150 GDIA 6 17.9 6.10E−07 P31153 METK2 3 8.9 6.60E−06 P31689 DNJA1 4 18.9 3.10E−07 P31942 HNRH3 4 15.3 2.10E−06 P33176 KINH 4 3.9 2.00E−04 P33240 CSTF2 3 6.6 1.20E−05 P33316 DUT 3 14.7 1.60E−06 P33991 MCM4 6 8.6 7.00E−06 P33993 MCM7 8 13.4 4.80E−05 P34897 GLYM 11 24 1.70E−06 P35221 CTNA1 3 5.7 7.60E−04 P35244 RFA3 2 33.1 2.70E−05 P35527 K1C9 1 2.2 6.80E−04 1 2.6 1.10E−04 P35908 K22E 2 4.4 1.10E−04 1 2.2 9.90E−06 P35998 PRS7 2 6.5 9.80E−06 P36405 ARL3 2 11.5 5.20E−04 P36551 HEM6 3 7.7 8.00E−05 P36776 LONM 5 8.2 8.40E−05 P36957 ODO2 2 3.8 3.60E−04 P37108 SRP14 2 18.4 8.50E−05 P38606 VATA 3 6 3.50E−04 P39656 OST48 3 8.1 2.10E−05 P39748 FEN1 2 5.8 0.002 P42765 THIM 2 8.3 6.80E−04 P45974 UBP5 2 2.6 2.00E−05 P46060 RAGP1 7 14.7 1.70E−06 P46459 NSF 2 2.7 0.0047 P46977 STT3A 2 4.3 3.20E−06 P47756 CAPZB 3 13.4 2.10E−06 P47897 SYQ 7 10.5 1.20E−04 P48047 ATPO 6 35.2 5.00E−06 P48444 COPD 2 4.3 7.00E−04 P48556 PSMD8 2 6.6 0.0043 P48735 IDHP 5 11.7 0.0012 P48739 PIPNB 2 8.1 5.50E−04 P49321 NASP 10 17.3 1.40E−06 P49588 SYAC 7 9.7 1.60E−04 P49721 PSB2 3 20.4 4.30E−05 P49736 MCM2 8 10.4 2.20E−04 P49755 TMEDA 2 12.8 1.30E−04 P49916 DNLI3 3 3.6 0.0062 P50213 IDH3A 4 12 2.30E−05 P50395 GDIB 11 30.1 6.10E−07 P50402 EMD 3 16.9 2.20E−05 P50570 DYN2 4 3.9 4.20E−04 P51114 FXR1 2 5 1.40E−07 P51149 RAB7A 8 50.2 1.00E−05 P51649 SSDH 2 3.7 0.0014 P52292 IMA2 6 14.9 4.10E−06 P52565 GDIR1 5 21.1 2.30E−07 P54105 ICLN 2 16 1.40E−04 P54577 SYYC 8 14.8 2.50E−04 P54727 RD23B 2 4.2 0.0044 P54819 KAD2 8 34.3 5.60E−05 P54886 P5CS 7 10.8 2.00E−08 P55010 IF5 2 4.4 0.0048 P55265 DSRAD 2 2.1 3.80E−04 P55884 EIF3B 11 15.4 6.60E−06 P56134 ATPK 2 25.5 1.70E−07 P56192 SYMC 3 4.1 2.40E−07 P60174 TPIS 13 57 1.20E−08 5 22 5.00E−04 P60228 EIF3E 10 26.5 4.90E−06 P60660 MYL6 5 38.4 5.20E−06 P61158 ARP3 2 5.5 5.70E−06 P61160 ARP2 3 9.6 9.90E−04 P61204 ARF3 7 47.5 8.30E−07 1 11 0.0015 P61513 RL37A 2 28.3 1.70E−07 P61619 S61A1 2 4.6 3.50E−04 P61758 PFD3 3 19.3 2.30E−04 P62195 PRS8 4 14 3.60E−04 P62241 RS8 8 47.1 4.60E−07 P62258 1433E 16 63.5 1.30E−08 1 11.4 0.0016 P62263 RS14 4 24.5 1.90E−06 1 7.3 1.20E−05 P62269 RS18 9 38.8 9.80E−06 P62306 RUXF 2 24.4 1.10E−05 P62491 RB11A 4 22.2 3.70E−05 P62714 PP2AB 3 11 4.00E−06 P62873 GBB1 3 9.7 1.90E−05 P62891 RL39 2 19.6 3.60E−04 P63220 RS21 4 42.2 3.90E−07 P63244 GBLP 9 36.9 1.20E−05 P78344 IF4G2 3 3.1 8.20E−04 P84103 SRSF3 6 31.7 5.40E−06 P84157 MXRA7 2 14.2 1.20E−05 P98179 RBM3 3 27.4 2.60E−04 Q00325 MPCP 5 10.8 2.90E−06 Q00526 CDK3 3 10.2 1.30E−04 Q00535 CDK5 2 6.5 0.0025 Q01081 U2AF1 2 10.8 8.30E−04 Q01085 TIAR 3 9.1 1.20E−04 Q01130 SRSF2 4 22.6 1.30E−07 Q01844 EWS 2 3.5 1.80E−04 Q02543 RL18A 4 18.2 3.40E−07 Q02809 PLOD1 3 5.9 0.0024 Q02978 M2OM 6 22.6 9.30E−06 Q04837 SSBP 5 38.5 9.80E−07 2 15.5 1.00E−03 Q06323 PSME1 2 8.4 9.00E−04 Q07020 RL18 6 31.4 3.90E−07 Q08752 PPID 2 4.9 0.0011 Q09028 RBBP4 6 13.9 5.40E−07 Q10471 GALT2 2 3.7 0.0014 Q10713 MPPA 2 5.3 0.0016 Q12874 SF3A3 4 9.6 6.60E−05 Q12904 AIMP1 2 7.7 0.0049 Q12907 LMAN2 2 8.4 4.80E−05 Q13011 ECH1 2 4.9 0.003 Q13242 SRSF9 3 14 5.70E−05 Q13347 EIF3I 7 22.2 3.10E−07 Q13509 TBB3 20 32.9 8.10E−08 Q13616 CUL1 2 2.4 5.80E−04 Q13620 CUL4B 3 3.2 0.0012 Q13867 BLMH 3 7 6.30E−04 Q14008 CKAP5 2 1.2 6.00E−04 Q14157 UBP2L 2 1.8 1.10E−04 Q14257 RCN2 2 10.1 1.20E−05 Q14444 CAPR1 8 12.3 1.80E−06 Q14566 MCM6 5 7.6 2.90E−06 Q14669 TRIPC 2 0.9 9.40E−04 Q14692 BMS1 2 1.4 1.50E−04 Q14697 GANAB 12 15.7 2.80E−07 Q14839 CHD4 5 3.2 2.00E−04 Q14974 IMB1 13 18.2 1.10E−07 Q15008 PSMD6 5 15.2 4.00E−05 Q15021 CND1 2 1.2 6.40E−04 Q15126 PMVK 2 10.9 5.80E−04 Q15269 PWP2 2 2.7 0.0028 Q15363 TMED2 2 10.9 3.00E−04 Q15427 SF3B4 2 7.3 1.30E−05 Q15637 SF01 2 5.8 5.30E−04 Q15691 MARE1 3 14.2 3.00E−06 Q15717 ELAV1 9 28.2 4.00E−07 Q15758 AAAT 2 4.4 1.30E−04 Q16555 DPYL2 2 2.4 0.0024 Q16576 RBBP7 6 13.6 5.40E−07 Q16629 SRSF7 4 17.6 4.20E−05 Q16630 CPSF6 3 8.7 2.20E−07 Q16658 FSCN1 3 8.9 2.50E−06 Q16718 NDUA5 3 29.3 4.00E−05 Q16836 HCDH 3 13.7 1.50E−05 Q16850 CP51A 2 4.8 6.70E−06 Q3ZCM7 TBB8 13 25.7 2.10E−07 1 3.2 0.0037 Q3ZCQ8 TIM50 2 7.6 7.20E−05 Q49A53 ARF1L 2 33.3 0.0065 Q53EL6 PDCD4 2 3.8 2.70E−04 Q58FF6 H90B4 6 10.1 1.70E−05 Q66LE6 2ABD 2 5.7 5.70E−06 Q6EEV6 SUMO4 2 23.2 4.70E−06 Q6NVY1 HIBCH 2 5.7 0.0027 Q6PI48 SYDM 2 3.3 1.80E−04 Q71UM5 RS27L 3 26.2 3.60E−05 Q7KZ85 SPT6H 2 1 1.70E−04 Q7L014 DDX46 2 2 2.10E−04 Q7L2H7 EIF3M 3 11 5.50E−05 Q86V81 THOC4 3 22.2 8.20E−06 Q8N983 RM43 2 10.2 0.0024 Q8NBS9 TXND5 2 4.4 3.10E−04 Q8NCW5 NNRE 3 13.5 5.00E−06 Q8TCS8 PNPT1 2 3.6 1.90E−04 Q8TEX9 IPO4 2 1.9 8.50E−05 Q8WUA2 PPIL4 2 5.5 3.50E−04 Q8WUM4 PDC6I 6 8.9 8.70E−05 Q8WXF1 PSPC1 4 9.4 3.50E−05 Q8WYA6 CTBL1 2 3 1.50E−04 Q92769 HDAC2 2 5.9 1.30E−07 Q92783 STAM1 2 5.9 9.20E−05 Q92900 RENT1 4 4.5 4.90E−06 Q92905 CSN5 7 25.4 2.70E−06 Q92973 TNPO1 3 3.6 2.20E−04 Q96AY3 FKB10 2 4.1 6.40E−04 1 4.5 9.10E−04 Q96CX2 KCD12 4 14.2 4.80E−06 Q96DV4 RM38 2 4.2 8.60E−04 Q96E17 RAB3C 2 11.5 9.40E−05 Q96EP5 DAZP1 2 7.6 8.20E−07 Q96ER9 CCD51 2 6.1 0.0014 Q96IX5 USMG5 2 44.8 5.20E−05 Q96T88 UHRF1 2 2.3 0.0016 Q99436 PSB7 2 10.5 8.30E−04 Q99536 VAT1 4 14.8 4.10E−05 Q99613 EIF3C 4 5 6.10E−06 Q99614 TTC1 3 13.4 5.00E−05 Q99714 HCD2 3 17.6 4.10E−05 Q99733 NP1L4 4 13.1 8.90E−06 Q99867 TBB4Q 8 17.5 2.10E−07 Q99878 H2A1J 20 80.5 2.90E−09 8 46.1 1.20E−07 10 48.4 2.00E−07 Q9BQ67 GRWD1 2 5.6 2.00E−05 Q9BSJ8 ESYT1 3 3.3 3.90E−05 Q9BUF5 TBB6 13 19.1 5.00E−07 1 3.1 0.0037 Q9BV20 MTNA 2 13 1.90E−04 Q9BVP2 GNL3 2 4.7 8.30E−04 Q9GZS3 WDR61 2 11.8 3.60E−06 Q9GZZ1 NAA50 2 11.2 5.20E−04 Q9H0D6 XRN2 2 2.7 0.0044 Q9H0L4 CSTFT 3 6.2 4.60E−06 Q9H0S4 DDX47 2 4.8 3.40E−04 Q9H0U4 RAB1B 4 23.9 9.40E−05 Q9H3N1 TMX1 2 7.5 3.40E−04 Q9H3U1 UN45A 2 2.9 0.0017 Q9H857 NT5D2 2 4 8.80E−05 Q9H9B4 SFXN1 3 8.4 8.60E−05 Q9HAV7 GRPE1 3 14.3 5.70E−04 Q9HC38 GLOD4 3 11.2 1.20E−04 Q9NRG9 AAAS 3 7.7 7.60E−06 Q9NRX2 RM17 2 9.7 0.0054 Q9NSD9 SYFB 6 10.9 2.00E−04 Q9NSE4 SYIM 2 2.1 5.10E−04 Q9NTJ5 SAC1 3 5.8 3.50E−04 Q9NTZ6 RBM12 2 1.7 9.10E−04 Q9NUU7 DD19A 2 4.6 4.40E−04 Q9NY12 GAR1 2 10.1 5.60E−04 Q9NZL9 MAT2B 2 6.6 9.60E−07 Q9P0M6 H2AW 2 6.2 0.0026 Q9UBB4 ATX10 2 5.7 3.50E−04 Q9UBT2 SAE2 2 3.1 1.60E−04 Q9UBX3 DIC 2 6.6 5.00E−05 Q9UG63 ABCF2 3 5.3 0.0029 Q9UHD8 SEPT9 2 4.8 0.0025 Q9UHV9 PFD2 3 22.7 1.90E−05 Q9UHX1 PUF60 2 4.5 5.00E−04 Q9UIG0 BAZ1B 2 1.5 6.80E−04 Q9UJZ1 STML2 3 11.8 2.40E−04 Q9UKD2 MRT4 3 11.7 0.0058 Q9UKK9 NUDT5 2 12.8 0.0011 Q9UKV3 ACINU 2 1.6 6.50E−04 Q9UN86 G3BP2 2 5.4 1.90E−06 Q9Y224 CN166 4 24.2 6.20E−06 Q9Y230 RUVB2 13 32.6 9.50E−07 Q9Y295 DRG1 3 9.5 9.90E−04 Q9Y2B0 CNPY2 2 17.6 5.30E−04 Q9Y3D9 RT23 3 15.8 2.00E−05 Q9Y5L4 TIM13 2 25.3 8.60E−06 Q9Y5S9 RBM8A 2 10.9 4.80E−06 Q9Y678 COPG1 2 3.3 1.30E−04 Q9Y6C9 MTCH2 2 5.6 0.0019 Q9Y6M1 IF2B2 2 4.5 9.10E−06

TABLE 9 Fold Category GO_ID GO_Description Count % PValue Enrichment FDR GOTERM_BP_FAT GO: 0022402 cell cycle process 47 8.1174439 3.53E−06 2.0762695 0.0061068 GO: 0045454 cell redox homeostasis 15 2.5906736 1.39E−07 5.9427166 2.40E−04 GO: 0034622 cellular macromolecular complex assembly 69 11.917098 3.88E−31 5.4157209 6.71E−28 GO: 0034621 cellular macromolecular complex subunit 73 12.607945 3.17E−31 5.1037448 5.48E−28 organization GO: 0043623 cellular protein complex assembly 24 4.1450777 1.21E−07 3.6976903 2.09E−04 GO: 0031497 chromatin assembly 36 6.2176166 1.37E−26 10.328032 2.38E−23 GO: 0006333 chromatin assembly or disassembly 41 7.0811744 1.86E−25 8.0577622 3.22E−22 GO: 0006325 chromatin organization 49 8.462867 9.82E−13 3.235479 1.70E−09 GO: 0051276 chromosome organization 62 10.708117 9.68E−16 3.1906874 1.73E−12 GO: 0006259 DNA metabolic process 45 7.7720207 1.03E−06 2.2197103 0.0017757 GO: 0006323 DNA packaging 39 6.7357513 8.72E−25 8.3198032 1.51E−21 GO: 0051236 establishment of RNA localization 17 2.9360967 1.35E−06 4.3743295 0.0023393 GO: 0006091 generation of precursor metabolites and 32 5.5267703 3.10E−06 2.5517607 0.0053624 energy GO: 0006007 glucose catabolic process 14 2.417962 3.50E−07 6.0246851 6.06E−04 GO: 0006096 glycolysis 12 2.0725389 1.78E−06 6.3726152 0.0030752 GO: 0019320 hexose catabolic process 14 2.417962 2.86E−06 5.064228 0.0049557 GO: 0006886 intracellular protein transport 36 6.2176166 2.64E−06 2.40251 0.0045756 GO: 0046907 intracellular transport 60 10.362694 3.97E−09 2.2793981 6.86E−06 GO: 0065003 macromolecular complex assembly 81 13.989637 2.21E−19 3.0401687 3.82E−16 GO: 0043933 macromolecular complex subunit organization 85 14.680484 7.15E−20 2.9880983 1.24E−16 GO: 0046365 monosaccharide catabolic process 14 2.417962 4.00E−06 4.9215737 0.0069237 GO: 0016071 mRNA metabolic process 63 10.880829 1.90E−22 4.2498454 3.28E−19 GO: 0006397 mRNA processing 58 10.017271 5.78E−22 4.5097999 1.00E−18 GO: 0034660 ncRNA metabolic process 33 5.6994819 6.77E−10 3.5811327 1.17E−06 GO: 0034470 ncRNA processing 25 4.3177893 4.39E−07 3.3368195 7.60E−04 GO: 0032269 negative regulation of cellular protein 23 3.9723661 3.02E−06 3.1892579 0.0052313 metabolic process GO: 0051248 negative regulation of protein metabolic 24 4.1450777 1.62E−06 3.2033467 0.0028 process GO: 0000398 nuclear mRNA splicing, via spliceosome 39 6.7357513 3.40E−20 6.3622024 5.88E−17 GO: 0051169 nuclear transport 24 4.1450777 7.55E−08 3.7913027 1.31E−04 GO: 0050657 nucleic acid transport 17 2.9360967 1.35E−06 4.3743295 0.0023393 GO: 0015931 nucleobase, nucleoside, nucleotide and nucleic 19 3.2815199 5.08E−07 4.1967149 8.80E−04 acid transport GO: 0006913 nucleocytoplasmic transport 24 4.1450777 5.94E−08 3.8399092 1.03E−04 GO: 0006334 nucleosome assembly 36 6.2176166 3.21E−27 10.69689 5.56E−24 GO: 0034728 nucleosome organization 37 6.3903282 1.30E−26 9.9300877 2.24E−23 GO: 0051351 positive regulation of ligase activity 14 2.417962 5.52E−06 4.7867361 0.0095539 GO: 0051443 positive regulation of ubiquitin-protein ligase 14 2.417962 3.39E−06 4.9918819 0.005867 activity GO: 0010608 posttranscriptional regulation of gene 33 5.6994819 7.06E−11 3.9036043 1.22E−07 expression GO: 0006457 protein folding 31 5.3540587 1.63E−11 4.371422 2.83E−08 GO: 0051258 protein polymerization 12 2.0725389 2.76E−06 6.1125085 0.0047839 GO: 0065004 protein-DNA complex assembly 36 6.2176166 8.57E−26 9.8740521 1.48E−22 GO: 0006417 regulation of translation 20 3.4542314 2.17E−06 3.6437094 0.0037532 GO: 0006986 response to unfolded protein 14 2.417962 4.00E−06 4.9215737 0.0069237 GO: 0022613 ribonucleoprotein complex biogenesis 35 6.044905 2.65E−14 4.8532185 4.59E−11 GO: 0042273 ribosomal large subunit biogenesis 8 1.3816926 1.70E−08 19.967528 2.94E−05 GO: 0042274 ribosomal small subunit biogenesis 8 1.3816926 4.52E−08 18.152298 7.82E−05 GO: 0042254 ribosome biogenesis 28 4.835924 2.38E−13 5.7283891 4.12E−10 GO: 0006403 RNA localization 18 3.1088083 4.06E−07 4.4926937 7.03E−04 GO: 0006396 RNA processing 90 15.544041 4.13E−31 4.106667 7.15E−28 GO: 0008380 RNA splicing 58 10.017271 1.02E−24 5.0973442 1.76E−21 GO: 0000375 RNA splicing, via transesterification reactions 39 6.7357513 3.40E−20 6.3622024 5.88E−17 GO: 0000377 RNA splicing, via transesterification reactions 39 6.7357513 3.40E−20 6.3622024 5.88E−17 with bulged adenosine as nucleophile GO: 0050658 RNA transport 17 2.9360967 1.35E−06 4.3743295 0.0023393 GO: 0016072 rRNA metabolic process 22 3.7996546 1.42E−10 5.7198647 2.45E−07 GO: 0006364 rRNA processing 22 3.7996546 6.03E−11 5.9685545 1.04E−07 GO: 0006412 translation 96 16.580311 7.62E−56 7.2389828 1.32E−52 GO: 0006414 translational elongation 66 11.398964 2.39E−66 16.310109 4.13E−63 GOTERM_CC_FAT GO: 0005832 chaperonin-containing T-complex 6 1.0362694 2.03E−06 21.273786 0.0028758 GO: 0000785 chromatin 42 7.253886 2.34E−18 5.2120777 3.32E−15 GO: 0044427 chromosomal part 56 9.671848 1.10E−16 3.6007445 1.55E−13 GO: 0005694 chromosome 66 11.398964 2.26E−19 3.5610469 3.20E−16 GO: 0005829 cytosol 188 32.469775 1.16E−58 3.5083086 1.65E−55 GO: 0022625 cytosolic large ribosomal subunit 27 4.6632124 4.73E−28 17.634849 6.71E−25 GO: 0044445 cytosolic part 61 10.535406 2.58E−44 9.9604241 3.66E−41 GO: 0022626 cytosolic ribosome 49 8.462867 1.82E−46 15.014216 2.58E−43 GO: 0022627 cytosolic small ribosomal subunit 22 3.7996546 2.05E−19 13.65068 2.91E−16 GO: 0031975 envelope 57 9.8445596 1.06E−08 2.2744482 1.51E−05 GO: 0030530 heterogeneous nuclear ribonucleoprotein 15 2.5906736 1.47E−17 21.899486 2.09E−14 complex GO: 0043232 intracellular non-membrane-bounded organelle 263 45.423143 1.84E−56 2.5144479 2.61E−53 GO: 0070013 intracellular organelle lumen 188 32.469775 3.06E−39 2.6228502 4.34E−36 GO: 0015934 large ribosomal subunit 31 5.3540587 1.41E−24 11.483611 2.00E−21 GO: 0042470 melanosome 30 5.1813472 3.38E−19 8.3660958 4.80E−16 GO: 0031974 membrane-enclosed lumen 189 32.642487 3.47E−37 2.5274084 4.93E−34 GO: 0031980 mitochondrial lumen 28 4.835924 4.33E−07 3.0614259 6.15E−04 GO: 0005759 mitochondrial matrix 28 4.835924 4.33E−07 3.0614259 6.15E−04 GO: 0042645 mitochondrial nucleoid 10 1.7271157 2.34E−06 8.0062637 0.0033233 GO: 0044429 mitochondrial part 49 8.462867 3.12E−06 2.043952 0.0044341 GO: 0005739 mitochondrion 76 13.126079 2.19E−06 1.7353043 0.0031087 GO: 0043228 non-membrane-bounded organelle 263 45.423143 1.84E−56 2.5144479 2.61E−53 GO: 0031981 nuclear lumen 145 25.043178 1.71E−26 2.4819417 2.42E−23 GO: 0009295 nucleoid 10 1.7271157 2.34E−06 8.0062637 0.0033233 GO: 0005730 nucleolus 87 15.025907 1.96E−21 3.0935377 2.79E−18 GO: 0005654 nucleoplasm 76 13.126079 3.57E−10 2.1386346 5.06E−07 GO: 0000786 nucleosome 31 5.3540587 1.41E−25 12.212729 2.01E−22 GO: 0031967 organelle envelope 57 9.8445596 9.57E−09 2.2817852 1.36E−05 GO: 0019866 organelle inner membrane 34 5.8721934 1.23E−06 2.5649246 0.0017425 GO: 0043233 organelle lumen 188 32.469775 7.95E−38 2.563764 1.13E−34 GO: 0048770 pigment granule 30 5.1813472 3.38E−19 8.3660958 4.80E−16 GO: 0000502 proteasome complex 13 2.2452504 4.53E−06 5.2893841 0.0064322 GO: 0032993 protein-DNA complex 34 5.8721934 2.71E−24 9.8123278 3.85E−21 GO: 0030529 ribonucleoprotein complex 136 23.488774 4.52E−75 6.5542539 6.41E−72 GO: 0033279 ribosomal subunit 53 9.1537133 3.11E−39 10.27679 4.41E−36 GO: 0005840 ribosome 66 11.398964 1.43E−39 7.618984 2.03E−36 GO: 0015935 small ribosomal subunit 23 3.9723661 1.45E−15 9.0610572 2.05E−12 GO: 0005681 spliceosome 35 6.044905 1.11E−18 6.5809061 1.58E−15

TABLE 10 Intra- P1 P1 sub- MS1 P1 P1 P1 Acces- Gene Exp Inter-subunit unit MS1 m/z z P1 m/z z ppm score P1 ev sion Name P1 Protein Name P1 Peptide P1 Modification Frac O60814, P0C0S5 484.9986 4 511.778 2 −2.9 18.8 2.00E−03 O60814 H2B1K Histone H2B type AVTKYTSAK (SEQ ID [Alkene@121] 1-K NO: 153) Fil, O60814, P0C0S8 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 O60814 H2B1K Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] Frac 1-K NO: 154) Fil, O60814, P0C0S8 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] Frac 155) Fil O60814, P0C0S8 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac, O60814, P0CG48 834.6972 4 909.011 2 −1.1 38.8 7.50E−08 O60814 H2B1K Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] Lys 1-K (SEQ ID NO: 156) Lys O60814, P20671 434.2124 3 314.674 2 −0.9 18.2 1.00E−01 P20671 H2A1D Histone H2A type GKQGGK (SEQ ID NO: [Alkene@6] 1-D 157) Lys O60814, P20671 516.2424 4 454.216 2 −2.3 23.9 1.20E−03 P20671 H2A1D Histone H2A type KGNYSER (SEQ ID NO: [Alkene@37] 1-D 158) Fil O60814, P62805 538.0886 5 335.697 2 −2.3 19.1 5.40E−02 P62805 H4 Histone H4 GGKGLGK (SEQ ID NO: [Alkene@9] 159) Frac O60814, P62805 504.7589 4 335.697 2 −2.3 19.3 2.20E−02 P62805 H4 Histone H4 GGKGLGK (SEQ ID NO: [Alkene@9] 159) Frac O60814, P62805 648.7487 5 612.345 2 −2.3 36.5 1.80E−05 P62805 H4 Histone H4 GGKGLGKGGAKR (SEQ [Alkene@9 = 29, ID NO: 160) Acetyl@13 = 29, Acetyl@17 = 65] Frac O60814, P62805 694.1724 5 725.910 2 0.2 33.1 3.20E−05 P62805 H4 Histone H4 GKGGKGLGKGGAKR [Acetyl@6 = 8, (SEQ ID NO: 161) Alkene@9 = 8, Acetyl@13 = 40, Acetyl@17 = 59] Frac O60814, P62805 522.5168 4 371.216 2 −0.9 12.8 6.20E−02 P62805 H4 Histone H4 GLGKGGAK (SEQ ID [Alkene@13] NO: 162) Frac O60814, P62805 739.6469 4 470.271 2 −2.5 18.3 1.20E−01 P62805 H4 Histone H4 GLGKGGAKR (SEQ ID [Acetyl@13&Alkene NO: 163|SEQ ID NO: @17|Acetyl@17& 206) Alkene@13] Frac O60814, Q6FI13 494.2473 4 314.674 2 −0.9 19.8 6.10E−02 Q6FI13 H2A2A Histone H2A type GKQGGK (SEQ ID NO: [Alkene@6] 2-A 157) Frac O60814, Q6FI13 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 O60814 H2B1K Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-K NO: 154) Frac O60814, Q6FI13 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q6FI13 H2A2A Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] 2-A 155) Frac O60814, Q6FI13 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 O60814 H2B1K Histone 2B type LLLPGELAKHAVSEGTK, [Alkene@109] 1-K (SEQ ID NO: 156) Fil O60814, Q71DI3 852.1877 4 695.353 2 −1.5 33.9 8.20E−05 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Frac O60814, Q71DI3 522.7735 4 371.725 2 −4.1 21.8 2.40E−03 Q71DI3 H32 Histone H3.2 KQLATK (SEQ ID NO: [Alkene@19] 165) Frac O60814, Q71DI3 694.3665 4 909.008 2 −4.4 32.2 2.00E−05 O60814 H2B1K Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-K (SEQ ID NO: 156) Fil P06899, P0C0S8 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil P06899, P0CG48 834.6972 4 909.011 2 −1.1 38.8 7.50E−08 P06899 H2B1J Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-J (SEQ ID NO: 156) Fil P06899, P62805 538.0886 5 335.697 2 −2.3 19.1 5.40E−02 P62805 H4 Histone H4 GGKGLGK (SEQ ID NO: [Alkene@9] 159) Frac P07197, P08670 525.5099 4 590.310 2 −2.5 32.1 1.50E−04 P08670 VIME Vimentin FANYIDKVR (SEQ ID [Alkene@120] NO: 166) Frac P07197, P08670 869.1570 4 1047.995 2 −0.6 48.9 1.60E−07 P08670 VIME Vimentin FANYIDKVR (SEQ ID [Alkene@120] NO: 166) Frac P07197, P08670 745.8425 4 434.685 2 −2.8 12.7 1.60E−01 P08670 VIME Vimentin GQGKSR (SEQ ID NO: [ThioIB@143] 167) Frac P07197, P08670 639.5882 4 564.797 2 −2.5 23.5 9.60E−04 P07197 NFM Neurofilament KLLEGEETR (SEQ ID [Alkene@403] medium NO: 168) polypeptide Frac P07197, P08670 880.8981 4 1047.992 2 −3.4 52.6 6.80E−07 P07197 NFM Neurofilament QKQASHAQLGDAYDQEIR [Gln->pyro- medium (SEQ ID NO: 169) Glu@138, polypeptide ThiolB@139] Frac P07197, P08670 786.1388 4 650.858 2 −1.5 37.9 4.60E−04 P07197 NFM Neurofilament TDISTALKEIR (SEQ ID [Alkene@271] medium NO: 170) polypeptide Frac P07197, P08670 712.3697 4 614.368 2 −1.6 28.2 8.20E−04 P08670 VIME Vimentin TLLIKTVETR (SEQ ID [Alkene@445] NO: 171) Frac P07900, P14625 867.6945 4 835.457 2 −3.1 41.1 7.60E−08 P07900 HS90A Heat shock ADLINNLGTIAKSGTK [ThiolB@112] protein HSP 90- (SEQ ID NO: 172) alpha Frac P08670, P08670 785.8627 4 789.878 2 3.3 11.5 1.50E+00 P08670 VIME Vimentin NLQEAEEWYKSK (SEQ [Alkene@292] ID NO: 173) Frac P0C0S5, Q71D13 620.3456 6 702.378 3 −2.4 13.2 1.90E+00 P0C0S5 H2AZ Histone H2A.Z ATIAGGGVIPHIHKSLIGK [ThiolB@116] (SEQ ID NO: 197) Lys P0C0S8, P23527 606.7844 4 667.336 2 −2.0 25.0 1.80E−04 P23527 H2B1O Histone H2B type KESYSIYVYK (SEQ ID [Alkene@35] 1-O NO: 175) Lys P0C0S8, P23527 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys P0C0S8, P23527 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 P23527 H2B1O Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-O (SEQ ID NO: 156) Lys P0C0S8, P58876 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 P58876 H2B1D Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-D NO: 154) Lys P0C0S8, P58876 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil P0C0S8, P62807 1044.5538 4 1079.606 2 3.2 16.3 2.10E−02 P0C0S8 H2A1 Histone H2A type 1 HLQLAIRNDEELNKLLGK [Alkene@96] (SEQ ID NO: 176) Frac P0C0S8, P62807 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-C/E/F/G/I NO: 154) Fil, P0C0S8, P62807 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] Frac 155) Fil P0C0S8, P62807 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac P0C0S8, P62807 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 P62807 H2B1C Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-C/E/F/G/I (SEQ ID NO: 156) Fil P0C0S8, Q16778 1044.5538 4 1079.606 2 3.2 16.3 2.10E−02 P0C0S8 H2A1 Histone H2A type 1 HLQLAIRNDEELNKLLGK [Alkene@96] (SEQ ID NO: 176) Fil P0C0S8, Q16778 606.7844 4 667.336 2 −2.0 25.0 1.80E−04 Q16778 H2B2E Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] 2-E 175) Fil, P0C0S8, Q16778 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] Frac 155) Frac P0C0S8, Q16778 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 Q16778 H2B2E Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 2-E (SEQ ID NO: 156) Fil P0C0S8, Q71DI3 645.8282 4 460.733 2 0.3 13.8 1.20E+00 P0C0S8 H2A1 Histone H2A type 1 KTESHHK (SEQ ID NO: [Alkene@120] 177) Frac P0C0S8, Q71DI3 606.8022 4 551.735 2 −2.6 10.0 5.50E−01 P0C0S8 H2A1 Histone H2A type 1 KTESHHK (SEQ ID NO: [ThiolB@120] 198) Fil P0C0S8, Q71DI3 782.2435 5 532.307 3 −2.1 23.1 1.40E−02 Q71DI3 H32 Histone H3.2 RVTIMPKDIQLAR (SEQ [Alkene@123] ID NO: 178) Frac P0C0S8, Q71DI3 938.5287 4 1057.139 2 −1.7 34.8 1.40E−06 P0C0S8 H2A1 Histone H2A type 1 VTIAQGGVLPNIQAVLLPKK [Alkene@119] (SEQ ID NO: 179) Lys P0C0S8, Q8N257 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys P0C0S8, Q93079 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 Q93079 H2B1H Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-H NO: 154) Lys P0C0S8, Q93079 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys P0C0S8, Q93079 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 Q93079 H2B1H Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-H (SEQ ID NO: 156) Fil P0C0S8, Q99877 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil P0C0S8, Q99879 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 Q99879 H2B1M Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-M NO: 154) Fil, P0C0S8, Q99879 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] Lys 155) Frac P0CG48, P62805 523.0272 4 376.675 2 −0.3 12.3 9.30E−01 P62805 H4 Histone H4 GGVKR (SEQ ID NO: [ThiolB@45] 180) Frac P0CG48, P62807 834.6972 4 909.011 2 −1.1 38.8 7.50E−08 P62807 H2B1C Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-C/E/F/G/I (SEQ ID NO: 156) Frac P0CG48, Q6FI13 557.7816 4 314.674 2 −0.9 12.0 8.80E−02 Q6FI13 H2A2A Histone H2A type GKQGGK (SEQ ID NO: [Alkene@6] 2-A 157) Frac P0CG48, Q71DI3 570.0469 4 660.372 2 −1.9 10.1 1.50E+00 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Alkene@6 = 26] NO: 314) Frac P0CG48, Q71DI3 706.6240 4 660.372 2 −1.9 28.2 4.50E−04 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Alkene@6 = 34] NO: 315) Frac P0CG48, Q71DI3 711.3011 4 759.376 2 2.3 21.8 5.90E−02 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Oxidation@1, NO: 316) ThiolB@6 = 36] Lys P20671, O60814 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 O60814 H2B1K Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-K (SEQ ID NO: 156) Lys P20671, Q71DI3 938.5287 4 1057.139 2 −1.7 34.8 1.40E−06 P20671 H2A1D Histone H2A type VTIAQGGVLPNIQAVLLPKK [Alkene@119] 1-D (SEQ ID NO: 179) Lys P23527, Q71DI3 852.1877 4 695.353 2 −1.5 33.9 8.20E−05 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Lys P23527, Q93077 606.7844 4 667.336 2 −2.0 25.0 1.80E−04 P23527 H2B1O Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] 1-O 175) Lys P23527, Q93077 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q93077 H2A1C Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] 1-C 155) Lys P23527, Q93077 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q93077 H2A1C Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] 1-C 155) Frac P62805, P62807 538.0886 5 335.697 2 −2.3 19.1 5.40E−02 P62805 H4 Histone H4 GGKGLGK (SEQ ID NO: [Alkene@9] 159) Frac P62805, P62807 536.0743 5 478.260 2 2.0 19.5 2.90E−02 P62807 H2B1C Histone H2B type LAHYNKR (SEQ ID NO: [Alkene@86] 1-C/E/F/G/I 181) Frac P62805, Q6FI13 657.5676 4 446.218 2 −3.6 24.6 6.20E−04 Q6FI13 H2A2A Histone H2A type KGNYAER (SEQ ID NO: [ThiolB@37] 2-A 199) Fil, P62805, Q71DI3 734.0969 4 672.829 2 −2.6 32.4 6.20E−05 P62805 H4 Histone H4 DAVTYTEHAKR (SEQ ID [Alkene@78] Frac, NO: 182) Lys Fil P62805, Q71DI3 766.1234 4 736.878 2 −0.3 21.7 1.10E−03 P62805 H4 Histone H4 DAVTYTEHAKRK (SEQ [Alkene@78] ID NO: 183) Frac P62805, Q71DI3 703.8565 4 695.353 2 −1.5 24.6 1.10E−02 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Frac P62805, Q71DI3 760.6363 4 695.352 2 −3.0 30.8 3.90E−04 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Lys P62805, Q93079 864.9775 4 720.931 2 −1.8 23.5 1.30E−03 P62805 H4 Histone H4 GVLKVFLENVIR (SEQ ID [Alkene@60] NO: 184) Frac P62807, Q6FI13 494.2473 4 314.674 2 −0.9 19.8 6.10E−02 Q6FI13 H2A2A Histone H2A type GKQGGK (SEQ ID NO: [Alkene@6] 2-A 157) Fil, P62807, Q6FI13 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] Frac 1-C/E/F/G/I NO: 154) Fil, P62807, Q6FI13 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q6FI13 H2A2A Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] Frac 2-A 155) Frac P62807, Q6FI13 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 P62807 H2B1C Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-C/E/F/G/I (SEQ ID NO: 156) Fil, P62807, Q71DI3 852.1877 4 695.353 2 −1.5 33.9 8.20E−05 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] Frac NO: 164) Frac P62807, Q71DI3 694.3665 4 909.008 2 −4.4 32.2 2.00E−05 P62807 H2B1C Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-C/E/F/G/I (SEQ ID NO: 156) Frac P62807, Q96KK5 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-C/E/F/G/I NO: 154) Frac P62807, Q96KK5 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q96KK5 H2A1H Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] 1-H 155) Frac P62807, Q96KK5 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 P62807 H2B1C Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-C/E/F/G/I (SEQ ID NO: 156) Frac Q13765, Q15149 526.2927 4 455.788 2 −16.0 20.4 1.70E−03 Q13765 NACA Nascent AKAVRALK (SEQ ID NO: [Alkene@194] polypeptide 185) associated complex subunit alpha Frac Q13765, Q15149 526.2927 4 455.788 2 −16.0 20.4 1.70E−03 Q15149 PLEC Plectin AKAVRALK (SEQ ID NO: [Alkene@194] 185) Frac Q6DN03, Q6FI13 606.7844 4 667.336 2 −2.0 25.0 1.80E−04 Q6DN03 H2B2C Putative histone KESYSIYVYK (SEQ ID NO: [Alkene@35] H2B type 2-C 175) Frac Q6FI13, Q71DI3 543.6813 5 460.732 2 −1.9 17.5 2.00E−02 Q6FI13 H2A2A Histone H2A type KTESHHK (SEQ ID NO: [Alkene@120] 2-A 177) Frac Q6F113, Q71DI3 512.4611 5 460.732 2 −1.9 15.4 1.10E−01 Q6FI13 H2A2A Histone H2A type KTESHHK (SEQ ID NO: [Alkene@120] 2-A 177) Frac Q6FI13, Q71DI3 606.8022 4 551.735 2 −2.6 10.0 5.50E−01 Q6FI13 H2A2A Histone H2A type KTESHHK (SEQ ID NO: [ThiolB@120] 2-A 198) Frac Q6FI13, Q71DI3 782.2435 5 532.307 3 −2.1 23.1 1.40E−02 Q71DI3 H32 Histone H3.2 RVTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 178) Frac Q6FI13, Q71DI3 785.4438 5 537.638 3 −3.2 22.7 2.10E−02 Q71DI3 H32 Histone H3.2 RVTIMPKDIQLAR (SEQ ID [Oxidation@121, NO: 200) Alkene@123] Frac Q6FI13, Q71DI3 942.5272 4 1057.139 2 −1.7 35.5 1.20E−07 Q6FI13 H2A2A Histone H2A type VTIAQGGVLPNIQAVLLPKK [Alkene@119] 2-A (SEQ ID NO: 179) Frac Q6FI13, Q99877 619.2982 4 660.328 2 −2.3 30.2 3.90E−05 Q99877 H2B1N Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-N NO: 154) Frac Q6FI13, Q99880 603.2783 4 660.328 2 −2.3 31.8 1.70E−05 Q99880 H2B1L Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-L NO: 154) Frac Q6FI13, Q99880 512.2441 4 446.219 2 −1.3 27.1 2.80E−03 Q6FI13 H2A2A Histone H2A type KGNYAER (SEQ ID NO: [Alkene@37] 2-A 155) Frac Q6FI13, Q99880 836.4354 4 909.010 2 −2.2 38.8 4.70E−08 Q99880 H2B1L Histone H2B type LLLPGELAKHAVSEGTK [Alkene@109] 1-L (SEQ ID NO: 156) Lys Q71DI3, Q93077 938.5287 4 1057.139 2 −1.7 34.8 1.40E−06 Q93077 H2A1C Histone H2A type VTIAQGGVLPNIQAVLLPKK [Alkene@119] 1-C (SEQ ID NO: 179) Lys Q71DI3, Q93079 852.1877 4 695.353 2 −1.5 33.9 8.20E−05 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Frac Q71DI3, Q96KK5 938.5287 4 1057.139 2 −1.7 34.8 1.40E−06 Q96KK5 H2A1H Histone H2A type VTIAQGGVLPNIQAVLLPKK [Alkene@119] 1-H (SEQ ID NO: 179) Frac Q71DI3, Q99880 852.1877 4 695.353 2 −1.5 33.9 8.20E−05 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID [Alkene@80] NO: 164) Frac O60814 537.0284 4 400.236 2 −3.1 25.1 2.80E−02 O60814 H2B1K Histone H2B type AVTKAQK (SEQ ID NO: [Alkene@21] 1-K 186) Frac O60814 649.3370 3 600.369 1 −4.2 12.7 2.00E−01 O60814 H2B1K Histone H2B type KAVTK (SEQ ID NO: 187) [Alkene@17] 1-K Fil, O60814 517.9415 3 391.692 2 −2.5 15.4 5.90E−01 O60814 H2B1K Histone H2B type KAVTK (SEQ ID NO: 201) [ThiolB@17] Lys 1-K Frac, O60814 619.2982 4 660.328 2 −2.3 30.2 3.90E−05 O60814 H2B1K Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] Lys 1-K NO: 154) Fil, P06733 598.3129 4 579.305 2 −1.8 32.8 3.20E−04 P06733 ENOA Alpha-enolase IEEELGSKAK (SEQ ID [Alkene@420] Frac, NO: 188) Lys Lys P06733 663.6019 4 685.860 2 −2.5 33.3 5.50E−03 P06733 ENOA Alpha-enolase LNVTEQEKIDK (SEQ ID [Alkene@89] NO: 189) Fil, P06733 541.2728 4 392.730 2 −4.6 11.1 9.00E−02 P06733 ENOA Alpha-enolase NVIKEK (SEQ ID NO: [Alkene@197] Lys 190) Frac P06748 643.3171 4 530.278 2 −1.5 29.4 6.80E−05 P06748 NPM Nucleophosmin AKMQASIEK (SEQ ID [ThiolB@250] NO: 191) Frac P06748 731.3334 3 514.754 2 0.0 11.7 9.20E−01 P06748 NPM Nucleophosmin DSKPSSTPR (SEQ ID [Alkene@215] NO: 192) Frac P06748 574.0543 4 464.287 2 4.9 20.9 5.10E−03 P06748 NPM Nucleophosmin LLSISGKR (SEQ ID NO: [Alkene@141] 193) Frac P06748 760.0324 3 656.341 2 −3.3 38.5 2.20E−05 P06748 NPM Nucleophosmin QEKTPK (SEQ ID NO: [Gln->pyro- 194) Glu@231, Alkene@233] Frac P06748 574.5322 4 392.710 2 −9.2 11.5 4.90E−02 P06748 NPM Nucleophosmin QEKTPK (SEQ ID NO: [Alkene@233] 202) Frac P06748 619.5454 4 482.740 2 −0.7 15.3 4.90E−02 P06748 NPM Nucleophosmin SKGQESFK (SEQ ID NO: [Alkene@223] 195) Frac P06748 472.9812 4 573.741 2 −5.1 10.3 1.30E−01 P06748 NPM Nucleophosmin SKGQESFK (SEQ ID NO: [ThiolB@223] 203) Fil P06899 517.9415 3 391.692 2 −2.5 15.4 5.90E−01 P06899 H2B1J Histone H2B type KAVTK (SEQ ID NO: 201) [ThiolB@17] 1-J Fil P06899 622.8040 4 667.338 2 1.0 26.8 1.90E−04 P06899 H2B1J Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] 1-J 175) Frac P07197 557.5172 4 500.258 2 −1.8 31.6 7.60E−04 P07197 NFM Neurofilament AEVGKGEQK (SEQ ID [Alkene@698] medium NO: 208) polypeptide Frac P07197 477.4917 4 390.734 2 −0.9 22.1 6.40E−03 P07197 NFM Neurofilament AKSPVPK (SEQ ID NO: [Alkene@614] medium 209) polypeptide Frac P07197 555.2757 4 390.733 2 −3.4 18.1 2.30E−02 P07197 NFM Neurofilament AKSPVPK (SEQ ID NO: [Alkene@614] medium 209) polypeptide Frac P07197 441.4798 4 390.734 2 −0.9 15.0 6.90E−02 P07197 NFM Neurofilament AKSPVPK (SEQ ID NO: [Alkene@614] medium 209) polypeptide Frac P07197 594.2940 3 769.407 1 −2.7 6.5 8.70E+00 P07197 NFM Neurofilament DVPEKK (SEQ ID NO: [Alkene@731] medium 210) polypeptide Frac P07197 788.3696 4 976.902 2 −1.0 15.7 1.80E−02 P07197 NFM Neurofilament EEEPEAEEEEVAAKK [ThiolB@509] medium (SEQ ID NO: 211) polypeptide Frac P07197 765.3303 4 620.313 2 −2.3 22.2 1.80E−03 P07197 NFM Neurofilament EEGKPLQQEK (SEQ ID [Alkene@766] medium NO: 212) polypeptide Frac P07197 757.3589 3 629.336 1 −0.9 3.6 1.10E−01 P07197 NFM Neurofilament GAKGSR (SEQ ID NO: [Alkene@793] medium 213) polypeptide Frac P07197 757.6872 3 629.334 1 −4.1 7.9 2.60E−02 P07197 NFM Neurofilament GAKGSR (SEQ ID NO: [Alkene@793] medium 213) polypeptide Frac P07197 533.4902 4 671.261 2 −2.8 26.8 1.20E−03 P07197 NFM Neurofilament GEQKEEEEK (SEQ ID [ThiolB@702] medium NO: 214) polypeptide Frac P07197 700.8235 4 452.205 2 −3.0 28.8 5.30E−03 P07197 NFM Neurofilament GGDKSEEK (SEQ ID NO: [Alkene@847] medium 215) polypeptide Frac P07197 540.5170 4 452.208 2 3.7 20.5 3.20E−02 P07197 NFM Neurofilament GGDKSEEK (SEQ ID NO: [Alkene@847] medium 215) polypeptide Frac P07197 473.9890 4 383.726 2 −1.4 22.0 3.50E−03 P07197 NFM Neurofilament GKSPVPK (SEQ ID NO: [Alkene@627] medium 216) polypeptide Frac P07197 552.2787 4 378.716 2 −0.4 22.4 4.70E−03 P07197 NFM Neurofilament GKSPVPK (SEQ ID NO: [Alkene@627] medium 216) polypeptide Frac P07197 554.7847 4 383.726 2 −1.4 13.3 5.00E−03 P07197 NFM Neurofilament GKSPVSK (SEQ ID NO: [Alkene@666] medium 217) polypeptide Frac P07197 774.6290 4 655.320 2 −4.2 10.1 5.30E−01 P07197 NFM Neurofilament GSPSTVSSSYKR (SEQ [Alkene@53] medium ID NO: 218) polypeptide Frac P07197 743.1202 4 940.426 2 −12.0 15.1 1.80E−01 P07197 NFM Neurofilament GWTNGLDLSPADEKK [Deamidated@832, medium (SEQ ID NO: 219) ThiolB@842] polypeptide Frac P07197 585.5341 4 720.391 1 −2.3 13.6 2.90E−01 P07197 NFM Neurofilament KDYLK (SEQ ID NO: [Alkene@259] medium 220) polypeptide Frac P07197 856.4033 4 564.797 2 −2.5 33.7 2.10E−05 P07197 NFM Neurofilament KLLEGEETR (SEQ ID [ThiolB@403] medium NO: 204) polypeptide Frac P07197 744.6050 4 763.893 2 −1.4 43.6 3.00E−05 P07197 NFM Neurofilament LTEAAEQNKEAIR (SEQ [Alkene@307] medium ID NO: 221) polypeptide Frac P07197 627.1050 5 854.894 2 −4.3 12.4 2.60E−01 P07197 NFM Neurofilament LTEAAEQNKEAIR (SEQ [ThiolB@307] medium ID NO: 222) polypeptide Frac P07197 439.4437 5 456.232 2 −1.0 10.6 2.10E+00 P07197 NFM Neurofilament LVSTKK (SEQ ID NO: [ThiolB@898] medium 223) polypeptide Frac P07197 705.3453 4 536.797 2 −1.6 28.1 1.50E−03 P07197 NFM Neurofilament SEEKVVVTK (SEQ ID [Alkene@851] medium NO: 224) polypeptide Frac P07197 664.5715 4 927.916 2 −5.4 21.6 7.40E−03 P07197 NFM Neurofilament SEEVATKEELVADAK [ThiolB@598] medium (SEQ ID NO: 225) polypeptide Frac P07197 574.0381 4 386.713 2 −1.6 21.0 6.70E−02 P07197 NFM Neurofilament SKAEVGK (SEQ ID NO: [Alkene@693] medium 226) polypeptide Frac P07197 616.3067 4 471.249 2 −3.3 29.9 1.90E−03 P07197 NFM Neurofilament SPVEEKAK (SEQ ID NO: [Alkene@677] medium 227) polypeptide Frac P07197 595.0430 4 464.242 2 −1.6 30.9 4.70E−03 P07197 NFM Neurofilament SPVEEKGK (SEQ ID NO: [Alkene@625] medium 228) polypeptide Frac P07197 789.7181 3 927.477 1 −1.3 17.1 2.50E−02 P07197 NFM Neurofilament SPVEEKGK (SEQ ID NO: [Alkene@625] medium 228) polypeptide Frac P07197 673.3341 4 625.834 2 −1.6 23.0 2.50E−03 P07197 NFM Neurofilament SPVPKSPVEEK (SEQ ID [Alkene@619] medium NO: 230) polypeptide Frac P07197 767.6319 4 864.888 2 1.2 21.5 4.20E−03 P07197 NFM Neurofilament TVEKITSEGGDGATK [ThiolB@860] medium (SEQ ID NO: 232) polypeptide Frac P07197 705.8660 4 419.754 2 −3.0 14.6 8.00E−02 P07197 NFM Neurofilament VEAPKLK (SEQ ID NO: [ThiolB@445] medium 233) polypeptide Frac P07197 645.0975 4 528.818 2 −1.1 28.2 3.00E−05 P07197 NFM Neurofilament VVVTKTVEK (SEQ ID [Alkene@856] medium NO: 234) polypeptide Frac P07900 871.6938 4 835.459 2 −0.7 33.9 1.60E−06 P07900 HS90A Heat shock ADLINNLGTIAKSGTK [Alkene@112] protein HSP 90- (SEQ ID NO: 205) alpha Frac P07910 515.2593 4 352.682 2 −0.9 17.8 2.40E−02 P07910 HNRPC Heterogeneous GSSKSGK (SEQ ID NO: [Alkene@184] nuclear 236) ribonucleoproteins C1/C2 Frac P07910 855.7723 3 457.270 2 −2.8 29.7 9.90E−03 P07910 HNRPC Heterogeneous KELTQIK (SEQ ID NO: [Alkene@198] nuclear 237) ribonucleoproteins C1/C2 Frac P07910 646.3376 4 457.270 2 −2.8 28.5 8.30E−03 P07910 HNRPC Heterogeneous KELTQIK (SEQ ID NO: [Alkene@198] nuclear 237) ribonucleoproteins C1/C2 Frac P07910 559.2748 4 457.271 2 −0.6 19.7 2.10E−02 P07910 HNRPC Heterogeneous KELTQIK (SEQ ID NO: [Alkene@198] nuclear 237) ribonucleoproteins C1/C2 Frac P08107 747.0454 3 743.392 1 −1.9 14.1 6.00E−01 P08107 HSP71 Heat shock 70 kDa DAKLDK (SEQ ID NO: [Alkene@325] protein 238) 1A/1B Fil, P08107 582.7902 4 536.292 2 −2.4 16.5 1.20E−01 P08107 HSP71 Heat shock 70 kDa ITITNDKGR (SEQ ID NO: [Alkene@507] Frac, protein 239) Lys 1A/1B Frac P08107 490.2351 4 529.279 2 −1.6 13.2 1.20E−01 P08107 HSP71 Heat shock 70 kDa LSKEEIER (SEQ ID NO: [Alkene@512] protein 240) 1A/1B Frac P08238 867.6945 4 835.457 2 −3.1 41.1 7.60E−08 P08238 HS90B Heat shock ADLINNLGTIAKSGTK [ThiolB@107] protein HSP 90- (SEQ ID NO: 172) beta Frac P08670 873.2054 4 590.310 2 −2.5 28.8 8.30E−05 P08670 VIME Vimentin FANYIDKVR (SEQ ID [Alkene@120] NO: 166) Frac P08670 675.1106 4 557.789 2 −2.8 31.2 1.60E−03 P08670 VIME Vimentin KLLEGEESR (SEQ ID [Alkene@402] NO: 241) Frac P08670 636.0847 4 557.790 2 −1.0 22.4 2.00E−03 P08670 VIME Vimentin KLLEGEESR (SEQ ID [Alkene@402] NO: 241) Frac P08670 844.4402 4 794.433 2 −2.6 34.2 8.50E−05 P08670 VIME Vimentin KVESLQEEIAFLK (SEQ [Alkene@223] ID NO: 242) Frac P08670 1098.7781 4 1276.136 2 −1.1 36.4 3.50E−06 P08670 VIME Vimentin LLQDSVDFSLADAINTEFK [Alkene@97] NTR (SEQ ID NO: 243) Frac P0C0S5 709.8815 4 641.710 3 −1.0 25.2 1.90E−04 P0C0S5 H2AZ Histone H2A.Z ATIAGGGVIPHIHKSLIGK [Alkene@116] (SEQ ID NO: 174) Frac P0C0S5 709.8815 4 641.710 3 −1.0 25.2 8.90E−04 P0C0S5 H2AZ Histone H2A.Z ATIAGGGVIPHIHKSLIGK [Alkene@116] (SEQ ID NO: 174) Frac P10412 607.3190 4 456.742 2 −2.0 21.4 1.10E−02 P10412 H14 Histone H1.4 AASGEAKPK (SEQ ID [Alkene@117] NO: 244) Fil P10412 392.2068 4 335.699 2 3.7 24.0 3.10E−02 P10412 H14 Histone H1.4 AGAAKAK (SEQ ID NO: [Alkene@127] 245) Fil P10412 560.0715 4 656.883 2 0.3 22.8 3.00E−03 P10412 H14 Histone H1.4 ERSGVSLAALKK (SEQ ID [Alkene@63] NO: 246) Frac P10412 630.0876 4 796.916 2 −2.0 32.6 1.90E−05 P10412 H14 Histone H1.4 GTLVQTKGTGASGSFK [Alkene@97] (SEQ ID NO: 247) Frac P10412 698.3719 4 796.915 2 −3.2 27.4 4.70E−05 P10412 H14 Histone H1.4 GTLVQTKGTGASGSFK [Alkene@97] (SEQ ID NO: 247) Frac P10412 724.3936 4 690.891 2 1.0 17.7 1.10E−02 P10412 H14 Histone H1.4 KASGPPVSELITK (SEQ [Alkene@34] ID NO: 248) Lys P10412 504.5979 3 343.695 2 −0.6 14.6 2.00E−01 P10412 H14 Histone H1.4 KSAGAAK (SEQ ID NO: [Alkene@26] 249) Fil P10809 691.8912 4 399.758 2 0.5 21.3 1.30E−03 P10809 CH60 60 kDa heat KGVITVK (SEQ ID NO: [Alkene@196] shock protein, 250) mitochondrial Fil P10809 480.4926 4 436.741 2 2.7 17.9 1.00E−01 P10809 CH60 60 kDa heat SIDLKDK (SEQ ID NO: [Alkene@87] shock protein, 251) mitochondrial Frac, P12277 433.2298 4 557.766 2 −2.2 20.1 3.40E−03 P12277 KCRB Creatine kinase FSEVLKR (SEQ ID NO: [ThiolB@313] Lys B-type 252) Lys P13639 678.1007 4 742.878 2 −0.3 37.9 1.10E−04 P13639 EF2 Elongation factor 2 FAAKGEGQLGPAER [Alkene@239] (SEQ ID NO: 253) Fil P14314 549.5410 4 471.755 2 2.0 18.9 2.60E−01 P14314 GLU2B Glucosidase 2 AREEKQK (SEQ ID NO: [Alkene@155] subunit beta 254) Fil P16403 560.0715 4 656.883 2 0.3 22.8 3.00E−03 P16403 H12 Histone H1.2 ERSGVSLAALKK (SEQ ID [Alkene@63] NO: 246) Frac P19338 965.2560 4 843.477 2 −0.3 31.6 1.70E−05 P19338 NUCL Nucleolin ALELTGLKVFGNEIK (SEQ [Alkene@370] ID NO: 255) Frac P19338 677.0848 4 646.299 2 −0.5 19.3 5.70E−04 P19338 NUCL Nucleolin GGKNSTWSGESK (SEQ [ThiolB@477] ID NO: 256) Frac P19338 491.5202 4 504.247 2 −3.3 17.1 6.00E−03 P19338 NUCL Nucleolin KAAVTPGK (SEQ ID NO: [ThiolB@80] 257) Frac, P19338 656.6004 4 605.328 2 −2.2 26.1 2.50E−04 P19338 NUCL Nucleolin SKGIAYIEFK (SEQ ID [Alkene@429] Lys NO: 258) Frac P20700 617.0859 4 527.317 2 −3.4 23.0 3.10E−04 P20700 LMNB1 Lamin-B1 AKLQIELGK (SEQ ID NO: [Alkene@102] 259) Frac P20700 621.8014 4 401.687 2 −2.8 10.3 4.90E−02 P20700 LMNB1 Lamin-B1 EKDNSR (SEQ ID NO: [Alkene@332] 260) Frac P20700 744.6227 4 576.299 2 −3.1 29.5 6.40E−05 P20700 LMNB1 Lamin-B1 KIGDTSVSYK (SEQ ID [Alkene@474] NO: 261) Lys P23527 622.8040 4 667.338 2 1.0 26.8 1.90E−04 P23527 H2B1O Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] 1-O 175) Lys P23527 1116.5245 4 667.339 2 2.5 21.3 3.60E−03 P23527 H2B1O Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] 1-O 175) Frac P24534 500.7666 4 390.752 2 −1.4 25.1 1.20E−03 P24534 EF1B Elongation factor KPALVAK (SEQ ID NO: [Alkene@133] 1-beta 262) Lys P27824 566.4846 5 339.190 2 −0.3 12.2 3.40E+00 P27824 CALX Calnexin HKNPK (SEQ ID NO: [Alkene@207] 263) Fil P30101 554.0370 4 396.220 2 3.7 20.7 2.40E−01 P30101 PDIA3 Protein disulfide- KFISDK (SEQ ID NO: [Alkene@147] isomerase A3 264) Fil P51572 650.5767 4 472.757 2 2.1 17.1 4.90E−03 P51572 BAP31 B-cell receptor- KQSEGLTK (SEQ ID NO: [Alkene@214] associated 265) protein 31 Frac P52272 869.1990 4 1066.508 2 −1.1 10.0 1.20E+00 P52272 HNRPM Heterogeneous GEIIAKQGGGGGGGSVPGI [ThiolB@388] nuclear ER (SEQ ID NO: 266) ribonucleoprotein M Frac P61353 652.0794 4 381.204 2 −1.0 10.4 1.90E−01 P61353 RL27 60S ribosomal FMKPGK (SEQ ID NO: [Alkene@6] protein L27 267) Frac P61353 656.0769 4 389.201 2 −2.1 9.0 9.30E−01 P61353 RL27 60S ribosomal FMKPGK (SEQ ID NO: [Oxidation@5, protein L27 268) Alkene@6] Fil P61604 676.8530 4 717.854 2 2.8 28.1 5.70E−05 P61604 CH10 10 kDa heat GKGGEIQPVSVK (SEQ [ThiolB@56] shock protein, ID NO: 269) mitochondrial Frac, P61978 746.0631 3 663.360 2 −3.4 27.8 2.40E−04 P61978 HNRPK Heterogeneous DLAGSIIGKGGQR (SEQ [Alkene@405] Lys nuclear ID NO: 271) ribonucleoprotein K Frac P61978 759.1172 4 1061.997 2 −1.0 27.8 7.20E−05 P61978 HNRPK Heterogeneous HESGASIKIDEPLEGSEDR [Alkene@422] nuclear (SEQ ID NO: 272) ribonucleoprotein K Fil, P62805 471.2395 3 362.659 2 −1.3 11.0 1.20E+00 P62805 H4 Histone H4 GGAKR (SEQ ID NO: [ThiolB@17] Frac, 273) Lys Frac, P62805 480.9111 3 341.650 2 4.2 10.4 4.50E−01 P62805 H4 Histone H4 GKGGK (SEQ ID NO: [ThiolB@6] Lys 274) Frac P62805 645.6061 4 470.271 2 −2.5 26.6 6.20E−03 P62805 H4 Histone H4 GLGKGGAKR (SEQ ID [Alkene@13 = 25, NO: 207) Acetyl@17 = 25] Frac P62807 537.0284 4 400.236 2 −3.1 25.1 2.80E−02 P62807 H2B1C Histone H2B type AVTKAQK (SEQ ID NO: [Alkene@21] 1-C/E/F/G/I 186) Frac P62807 649.3370 3 600.369 1 −4.2 12.7 2.00E−01 P62807 H2B1C Histone H2B type KAVTK (SEQ ID NO: 187) [Alkene@17] 1-C/E/F/G/I Frac P62807 517.9415 3 391.692 2 −2.5 15.4 5.90E−01 P62807 H2B1C Histone H2B type KAVTK (SEQ ID NO: 201) [ThiolB@17] 1-C/E/F/G/I Frac P62807 607.2775 4 660.329 2 −0.8 28.6 1.10E−04 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-C/E/F/G/I NO: 154) Fil, P62807 619.2982 4 660.328 2 −2.3 30.2 3.90E−05 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] Frac 1-C/E/F/G/I NO: 154) Frac P62807 1113.2683 4 660.327 2 −3.8 18.7 5.80E−03 P62807 H2B1C Histone H2B type KESYSVYVYK (SEQ ID [Alkene@35] 1-C/E/F/G/I NO: 154) Fil P62807 680.0826 4 478.260 2 2.0 17.5 1.00E−01 P62807 H2B1C Histone H2B type LAHYNKR (SEQ ID NO: [Alkene@86] 1-C/E/F/G/I 181) Lys P62826 697.0198 6 872.439 2 0.4 32.0 3.40E−06 P62826 RAN GTP-binding GPIKFNVWDTAGQEK [Alkene@60] nuclear protein (SEQ ID NO: 275) Ran Fil, P62841 531.4732 5 512.609 3 −0.9 28.4 3.30E−04 P62841 RS15 40S ribosomal KEAPPMEKPEWK (SEQ [Alkene@65 = 48] Lys protein S15 ID NO: 276) Lys P62937 657.3184 4 747.335 2 −1.6 27.2 1.20E−04 P62937 PPIA Peptidyl-prolyl ALSTGEKGFGYK (SEQ [ThiolB@44] cis-trans ID NO: 278) isomerase A Frac Q00839 536.2779 4 407.736 2 −2.7 23.5 1.30E−01 Q00839 HNRPU Heterogeneous LSDKGLK (SEQ ID NO: [Alkene@28] nuclear 279) ribonucleoprotein U Fil, Q00839 524.4593 5 413.232 2 −1.2 13.4 3.10E−01 Q00839 HNRPU Heterogeneous QRTQKK (SEQ ID NO: [Gln->pyro- Frac nuclear 280) Glu@615, ribonucleoprotein U Alkene@619] Frac Q02878 791.1782 4 754.916 2 −4.7 31.8 9.10E−04 Q02878 RL6 60S ribosomal IDQKAVDSQILPK (SEQ [Alkene@251] protein L6 ID NO: 281) Frac Q14103 679.0915 4 906.478 2 −2.8 31.0 1.70E−04 Q14103 HNRPD Heterogeneous IFVGGLSPDTPEEKIR [Alkene@197] nuclear (SEQ ID NO: 282) ribonucleoprotein D0 Frac Q15149 704.1021 4 609.311 2 −1.1 22.4 2.70E−03 Q15149 PLEC Plectin AQFEQLKDGK (SEQ ID [Alkene@3469] NO: 283) Frac Q15149 694.8314 4 702.857 2 −3.6 33.9 5.30E−04 Q15149 PLEC Plectin ASFAEKTAQLER (SEQ ID [ThiolB@1725] NO: 284) Frac Q15149 729.1006 4 528.277 2 −1.2 19.0 6.40E−02 Q15149 PLEC Plectin EAKELQQR (SEQ ID NO: [Alkene@1528] 285) Frac Q15149 689.3405 4 549.792 2 −2.0 30.2 3.40E−05 Q15149 PLEC Plectin KAALEEVER (SEQ ID [Alkene@2142] NO: 266) Frac Q15233 462.7337 4 588.264 2 −1.4 9.6 2.00E−01 Q15233 NONO Non-POU DKGFGFIR (SEQ ID NO: [ThiolB@109] domain- 287) containing octamer-binding protein Frac Q16778 537.0284 4 400.236 2 −3.1 25.1 2.80E−02 Q16778 H2B2E Histone H2B type AVTKAQK (SEQ ID NO: [Alkene@21] 2-E 186) Fil, Q16778 622.8040 4 667.338 2 1.0 26.8 1.90E−04 Q16778 H2B2E Histone H2B type KESYSIYVYK (SEQ ID NO: [Alkene@35] Frac 2-E 175) Frac Q6FI13 467.7418 4 349.718 2 −3.0 16.0 3.20E−01 Q6FI13 H2A2A Histone H2A type ARAKAK (SEQ ID NO: [Alkene@14] 2-A 288) Frac Q71DI3 485.5123 4 371.726 2 −1.4 21.5 3.70E−02 Q71DI3 H32 Histone H3.2 KQLATK (SEQ ID NO: 165) [Alkene@19] Lys Q71DI3 482.0097 4 371.726 2 −1.4 22.6 3.70E−02 Q71DI3 H32 Histone H3.2 KQLATK (SEQ ID NO: 165) [Alkene@19] Fil, Q71DI3 425.7235 4 371.726 2 −1.4 20.9 2.30E−02 Q71DI3 H32 Histone H3.2 KQLATK (SEQ ID NO: 165) [Alkene@19] Frac, Lys Frac Q71DI3 562.2980 4 371.726 2 −1.4 22.0 4.90E−04 Q71DI3 H32 Histone H3.2 KQLATK (SEQ ID NO: 165) [Alkene@19] Frac Q71DI3 567.0562 4 541.818 2 −2.7 27.4 1.50E−04 Q71DI3 H32 Histone H3.2 KQLATKAAR (SEQ ID [Alkene@19 = 48, NO: 289) Acetyl@24 = 48] Frac Q71DI3 570.5511 4 541.819 2 −0.9 29.7 6.50E−04 Q71DI3 H32 Histone H3.2 KQLATKAAR (SEQ ID [Alkene@19 = 36, NO: 290) Acetyl@24 = 36] Frac, Q71DI3 510.7692 4 541.819 2 −0.9 30.1 1.90E−04 Q71DI3 H32 Histone H3.2 KQLATKAAR (SEQ ID [Alkene@19 = 57, Lys NO: 291) Acetyl@24 = 57] Fil Q71DI3 689.0198 3 485.272 2 0.4 18.1 9.10E−04 Q71DI3 H32 Histone H3.2 KSAPATGGVK (SEQ ID [Alkene@28] NO: 292) Frac Q71DI3 397.9483 4 316.175 2 2.8 15.4 1.00E−01 Q71DI3 H32 Histone H3.2 KSTGGK (SEQ ID NO: [Alkene@10] 293) Frac Q71DI3 599.8130 4 379.710 2 −3.7 17.5 9.00E−02 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Frac Q71DI3 566.7612 4 379.711 2 −1.1 18.6 1.90E−02 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Lys Q93079 517.9415 3 391.692 2 −2.5 15.4 5.90E−01 Q93079 H2B1H Histone H2B type KAVTK (SEQ ID NO: 201) [ThiolB@17] 1-H Fil Q99877 517.9415 3 391.692 2 −2.5 15.4 5.90E−01 Q99877 H2B1N Histone H2B type KAVTK (SEQ ID NO: 201) [ThiolB@17] 1-N Fil Q99877 680.0826 4 478.260 2 2.0 17.5 1.00E−01 Q99877 H2B1N Histone H2B type LAHYNKR (SEQ ID NO: [Alkene@86] 1-N 181) Frac Q9NVA2 500.2460 4 423.247 2 −1.5 21.6 2.80E−03 Q9NVA2 SEPT11 Septin-11 FDLLKR (SEQ ID NO: [Alkene@371] 441) P2 P2 P2 P2 Gene Exp P2 m/z P2 z ppm score P2 ev Accession Name P2 Protein Name P2 Peptide P2 Modification Frac 358.208 2 −1.4 13.1 5.70E−02 P0C0S5 H2AZ Histone H2A.Z TKAVSR (SEQ ID NO: [Alkene@16] 296) Fil, Frac 446.218 2 −3.6 27.5 1.10E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil, Frac 478.258 2 −2.2 27.0 8.60E−03 O60814 H2B1K Histone H2B type 1-K LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil 478.258 2 −2.2 27.0 8.60E−03 O60814 H2B1K Histone H2B type 1-K SRKESYSVYVYK (SEQ ID [Alkene@35] NO: 297) Frac, Lys 660.373 2 −0.3 34.4 5.40E−05 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Alkene@6] NO: 317) Lys 328.143 2 −0.4 4.7 1.00E+00 O60814 H2B1K Histone H2B type 1-K KGSK (SEQ ID NO: [ThiolB@13] 298) Lys 478.258 2 −2.2 21.5 1.90E−01 O60814 H2B1K Histone H2B type 1-K LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil 667.011 3 −2.7 12.8 3.10E−01 O60814 H2B1K Histone H2B type 1-K LLLPGELAKHAVSEGTK [ThiolB@109] (SEQ ID NO: 299) Frac 664.815 2 0.2 14.7 1.60E−02 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, ThiolB@6] ID NO: 300) Frac 606.342 3 −2.9 16.4 2.50E−01 O60814 H2B1K Histone H2B type 1-K LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 909.010 2 −2.2 26.4 2.70E−03 O60814 H2B1K Histone H2B type 1-K LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 573.811 2 −0.6 19.5 2.60E−03 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] ID NO: 301) Frac 909.011 2 −1.1 34.0 7.40E−07 O60814 H2B1K Histone H2B type 1-K LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 573.809 2 −4.0 28.6 9.10E−05 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] ID NO: 301) Frac 446.218 2 −3.6 27.5 1.10E−03 Q6FI13 H2A2A Histone H2A type 2-A KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac 478.258 2 −2.2 27.0 8.60E−03 O60814 H2B1K Histone H2B type 1-K LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 663.847 2 −2.4 40.0 3.00E−05 Q6FI13 H2A2A Histone H2A type 2-A NDEELNKLLGK (SEQ ID [Alkene@96] NO. 302) Fil 909.011 2 −1.1 31.3 4.90E−06 O60814 H2B1K Histone H2B type 1-K LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 664.814 2 −1.3 10.9 3.40E−01 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, ThiolB@6] ID NO: 300) Frac 379.711 2 −1.1 19.5 3.90E−03 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Fil 478.258 2 −2.2 27.0 8.60E−03 P06899 H2B1J Histone H2B type 1-J LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil 660.373 2 −0.3 34.4 5.40E−05 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Alkene@6] NO: 317) Fil 667.011 3 −2.7 12.8 3.10E−01 P06899 H2B1J Histone H2B type 1-J LLLPGELAKHAVSEGTK [ThiolB@109] (SEQ ID NO: 299) Frac 360.699 2 −2.7 16.5 1.60E−01 P07197 NFM Neurofilament medium KDYLK (SEQ ID NO: [Alkene@259] polypeptide 220) Frac 590.310 2 −2.5 31.2 2.60E−04 P07197 NFM Neurofilament medium KQASHAQLGDAYDQEIR [Gln->pyro-Glu@138, Alkene@139] polypeptide (SEQ ID NO: 169) Frac 1047.993 2 −2.5 57.2 3.10E−08 P07197 NFM Neurofilament medium QKQASHAQLGDAYDQEIR [Gln->pyro-Glu@138, Alkene@139] polypeptide (SEQ ID NO: 169) Frac 614.368 2 −1.6 21.4 2.80E−03 P08670 VIME Vimentin TLLIKTVETR (SEQ ID NO: [Alkene@445] 171) Frac 614.367 2 −3.3 32.9 2.90E−04 P08670 VIME Vimentin TLLIKTVETR (SEQ ID NO: [Alkene@445] 171) Frac 821.406 2 −1.9 27.9 1.20E−04 P08670 VIME Vimentin TNEKVELQELNDR (SEQ [Alkene@104] ID NO: 303) Frac 801.360 2 −3.7 17.8 1.10E−02 P07197 NFM Neurofilament medium YAKLTEAAEQNK (SEQ ID [ThiolB@298] polypeptide NO: 304) Frac 799.920 2 −3.6 31.5 1.40E−04 P14625 ENPL Endoplasmin ELISNASDALDKIR (SEQ [Alkene@114] ID NO: 306) Frac 681.834 2 −3.0 31.4 1.20E−04 P08670 VIME Vimentin SKFADLSEAANR (SEQ ID [Alkene@294] NO: 308) Frac 532.307 3 −2.1 17.4 4.40E−02 Q71DI3 H32 Histone H3.2 RVTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 178) Lys 446.221 2 3.2 22.7 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys 478.258 2 −2.2 27.0 8.60E−03 P23527 H2B1O Histone H2B type 1-O LAHYNKR (SEQ ID NO: [Alkene@86] 181) Lys 663.847 2 −2.4 40.0 3.00E−05 P0C0S8 H2A1 Histone H2A type 1 NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Lys 446.218 2 −3.6 27.5 1.10E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys 478.258 2 −2.2 27.0 8.60E−03 P58876 H2B1D Histone H2B type 1-D LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil 909.015 2 3.3 17.7 5.50E−03 P62807 H2B1C Histone H26 type 1- LLLPGELAKHAVSEGTK [Alkene@109] C/E/F/G/I (SEQ ID NO: 156) Frac 446.218 2 −3.6 27.5 1.10E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil, Frac 478.258 2 −2.2 27.0 8.60E−03 P62807 H2B1C Histone H26 type 1- LAHYNKR (SEQ ID NO: [Alkene@86] C/E/F/G/I 181) Fil 478.258 2 −2.2 27.0 8.60E−03 P62807 H2B1C Histone H26 type 1- SRKESYSVYVYK (SEQ ID [Alkene@35] C/E/F/G/I NO: 297) Frac 663.847 2 −2.4 40.0 3.00E−05 P0C0S8 H2A1 Histone H2A type 1 NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Fil 909.015 2 3.3 17.7 5.50E−03 Q16778 H2B2E Histone H26 type 2-E LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Fil 446.221 2 3.2 22.7 2.80E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil, Frac 478.258 2 −2.2 27.0 8.60E−03 Q16778 H2B2E Histone H26 type 2-E LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 663.847 2 −2.4 40.0 3.00E−05 P0C0S8 H2A1 Histone H2A type 1 NDEELNKLLGK (SEQ D [Alkene@96] NO: 302) Fil 730.917 2 3.2 16.6 2.40E−01 Q71DI3 H32 Histone H3.2 RYQKSTELLIR (SEQ ID [Alkene@57] NO: 309) Frac 652.863 2 −1.7 22.4 9.30E−03 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [Alkene@57] NO: 310) Fil 1057.134 2 −6.4 38.1 7.20E−07 P0C0S8 H2A1 Histone H2A type 1 VTIAQGGVLPNIQAVLLPKK [Alkene@119] (SEQ ID NO: 179) Frac 719.907 2 −1.3 33.1 1.10E−03 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Lys 478.258 2 −2.2 27.0 8.60E−03 Q8N257 H2636 Histone H26 type 3-B LAHYNKR (SEQ ID NO: [Alkene@86] 181) Lys 446.218 2 −3.6 27.5 1.10E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys 478.258 2 −2.2 27.0 8.60E−03 Q93079 H2B1H Histone H26 type 1-H LAHYNKR (SEQ ID NO: [Alkene@86] 181) Lys 663.847 2 −2.4 40.0 3.00E−05 P0C0S8 H2A1 Histone H2A type 1 NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Fil 478.258 2 −2.2 27.0 8.60E−03 Q99877 H2B1N Histone H26 type 1-N LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil 446.218 2 −3.6 27.5 1.10E−03 P0C0S8 H2A1 Histone H2A type 1 KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil, Lys 478.258 2 −2.2 27.0 8.60E−03 Q99879 H2B1M Histone H26 type 1-M LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 751.375 2 −2.4 21.2 7.90E−02 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [ThiolB@6 = 22] NO: 318) Frac 660.373 2 −0.3 34.4 5.40E−05 P0CG48 UBC Polyubiquitin-C MQIFVKTLTGK (SEQ ID [Alkene@6] NO: 317) Frac 700.882 2 2.5 22.0 8.80E−03 P0CG48 UBC Polyubiquitin-C LIFAGKQLEDGR (SEQ ID [Alkene@48] NO: 319) Frac 379.711 2 −1.1 15.0 1.10E−02 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Frac 652.863 2 −1.7 26.8 6.00E−03 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [Alkene@57] NO: 310) Frac 652.863 2 −1.7 26.0 4.00E−04 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [Alkene@57] NO: 310) Lys 663.847 2 −2.4 40.0 3.00E−05 P20671 H2A1D Histone H2A type 1-D NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Lys 719.907 2 −1.3 33.1 1.10E−03 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Lys 909.011 2 −1.1 31.3 4.90E−06 P23527 H2B1O Histone H2B type 1-O LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Lys 446.221 2 3.2 22.7 2.80E−03 Q93077 H2A1C Histone H2A type 1-C KGNYAER (SEQ ID NO: [Alkene@37] 155) Lys 478.258 2 −2.2 27.0 8.60E−03 P23527 H2B1O Histone H2B type 1-O LAHYNKR (SEQ ID NO: [Alkene@86] 181) Lys 478.258 2 −2.2 27.0 8.60E−03 P23527 H2B10 Histone H2B type 1-O LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 667.011 3 −2.7 12.8 3.10E−01 P62807 H2B1C Histone H2B type 1- LLLPGELAKHAVSEGTK [ThiolB@109] C/E/F/G/I (SEQ ID NO: 299) Frac 507.611 3 2.8 19.1 6.40E−03 P62805 H4 Histone H4 TVTAMDVVYALKR (SEQ [Alkene@92] ID NO: 320) Frac 768.905 2 −4.1 27.0 9.20E−04 P62805 H4 Histone H4 TVTAMDVVYALKR (SEQ [Oxidation@85, Alkene@92] ID NO: 321) Fil, Frac, 695.352 2 −3.0 33.1 2.10E−04 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID NO: [Alkene@80] Lys 164) Fil 695.355 2 1.3 19.6 6.40E−03 Q71DI3 H32 Histone H3.2 EIAQDFKTDLR (SEQ ID NO: [Alkene@80] 164) Frac 612.344 2 3.9 34.5 1.30E−04 P62805 H4 Histone H4 GGKGLGKGGAKR (SEQ [Alkene@9 = 18, Acetyl@13 = 18, ID NO: 160) Acetyl@17 = 45] Frac 725.907 2 −4.0 32.1 5.80E−04 P62805 H4 Histone H4 GKGGKGLGKGGAKR [Acetyl@13 = 27, Acetyl@17 = 55, (SEQ ID NO: 322) Acetyl@6&Alkene@9|Acetyl @9&Alkene @6] Lys 909.011 2 −1.1 21.4 1.90E−04 Q93079 H2B1H Histone H2B type 1-H LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 573.809 2 −4.0 28.6 9.10E−05 P62807 H2B1C Histone H2B type 1- MPEPAKSAPARK (SEQ [Met-loss@1, Alkene@6] C/E/F/G/I ID NO: 301) Fil, Frac 446.218 2 −3.6 27.5 1.10E−03 Q6FI13 H2A2A Histone H2A type 2-A KGNYAER (SEQ ID NO: [Alkene@37] 155) Fil, Frac 478.258 2 −2.2 27.0 8.60E−03 P62807 H2B1C Histone H2B type 1- LAHYNKR (SEQ ID NO: [Alkene@86] C/E/F/G/I 181) Frac 663.847 2 −2.4 40.0 3.00E−05 Q6FI13 H2A2A Histone H2A type 2-A NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Fil, Frac 909.011 2 −1.1 31.3 4.90E−06 P62807 H2B1C Histone H2B type 1- LLLPGELAKHAVSEGTK [Alkene@109] C/E/F/G/I (SEQ ID NO: 156) Frac 379.711 2 −1.1 19.5 3.90E−03 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Frac 446.218 2 −3.6 27.5 1.10E−03 Q96KK5 H2A1H Histone H2A type 1-H KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac 478.258 2 −2.2 27.0 8.60E−03 P62807 H2B1C Histone H2B type 1- LAHYNKR (SEQ ID NO: [Alkene@86] C/E/F/G/I 181) Frac 663.847 2 −2.4 40.0 3.00E−05 Q96KK5 H2A1H Histone H2A type 1-H NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Frac 496.784 2 −2.9 26.5 6.50E−05 Q15149 PLEC Plectin GHLSGLAKR (SEQ ID [Alkene@923] NO: 323) Frac 496.784 2 −2.9 26.5 6.50E−05 Q13765 NACA Nascent polypeptide- GHLSGLAKR (SEQ ID [Alkene@923] associated complex NO: 323) subunit alpha Frac 446.221 2 3.2 22.7 2.80E−03 Q6FI13 H2A2A Histone H2A type 2-A KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac 532.308 3 −0.2 21.2 5.70E−03 Q71DI3 H32 Histone H3.2 RVTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 178) Frac 480.274 3 −0.8 16.2 1.80E−01 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Frac 652.863 2 −1.7 22.4 9.30E−03 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [Alkene@57] NO: 310) Frac 1057.134 2 −6.4 38.1 7.20E−07 Q6FI13 H2A2A Histone H2A type 2-A VTIAQGGVLPNIQAVLLPKK [Alkene@119] (SEQ ID NO: 179) Frac 1148.143 2 −1.2 20.3 1.70E−03 Q6FI13 H2A2A Histone H2A type 2-A VTIAQGGVLPNIQAVLLPKK [ThiolB@119] (SEQ ID NO: 324) Frac 727.903 2 −3.3 27.4 1.10E−03 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Oxidation@121, Alkene@123] NO: 313) Frac 478.258 2 −2.2 26.6 1.30E−02 Q6FI13 H2A2A Histone H2A type 2-A KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac 446.218 2 −3.6 27.5 1.10E−03 Q6FI13 H2A2A Histone H2A type 2-A KGNYAER (SEQ ID NO: [Alkene@37] 155) Frac 478.258 2 −2.2 27.0 8.60E−03 Q99880 H2B1L Histone H2B type 1-L LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 663.847 2 −2.4 40.0 3.00E−05 Q6FI13 H2A2A Histone H2A type 2-A NDEELNKLLGK (SEQ ID [Alkene@96] NO: 302) Lys 719.907 2 −1.3 33.1 1.10E−03 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Lys 909.011 2 −1.1 31.3 4.90E−06 Q93079 H2B1H Histone H2B type 1-H LLLPGELAKHAVSEGTK [Alkene@109] (SEQ ID NO: 156) Frac 719.907 2 −1.3 33.1 1.10E−03 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Frac 909.011 2 −1.1 31.3 4.90E−06 Q99880 H2B1L Histone H2B type 1-L LLLPGELAKHAVSEGTK [ThiolB@109] (SEQ ID NO: 299) Frac 573.809 2 −4.0 24.8 5.40E−05 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] ID NO: 301) Frac 573.808 2 −5.8 21.4 1.20E−03 O60814 H2B1K Histone H2B type 1-K MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] ID NO: 301) Fil, Lys 467.721 2 −2.7 10.0 8.30E−01 O60814 H2B1K Histone H2B type 1-K SAPAPKK (SEQ ID NO: [ThiolB@12] 325) Frac, Lys 478.258 2 −2.2 26.6 1.30E−02 O60814 H2B1K Histone H2B type 1-K LAHYNKR (SEQ ID NO: [Alkene@86] 181) Fil, Frac, 517.310 2 −2.5 31.5 1.20E−03 P06733 ENOA Alpha-enolase MSILKIHAR (SEQ ID [Met-loss + Acetyl@1, Alkene@5] Lys NO: 326) Lys 632.337 2 −1.6 13.6 9.30E−02 P06733 ENOA Alpha-enolase TIAPALVSKK (SEQ ID [ThiolB@80] NO: 327) Fil, Lys 589.806 2 −0.4 16.5 3.50E−03 P06733 ENOA Alpha-enolase TAIGKAGYTDK (SEQ ID [Alkene@233] NO: 328) Frac 656.340 2 −4.8 21.9 6.10E−03 P06748 NPM Nucleophosmin TPKGPSSVEDIK (SEQ ID [Alkene@239] NO: 329) Frac 573.743 2 −1.6 11.5 1.40E−02 P06748 NPM Nucleophosmin SKGQESFK (SEQ ID NO: [ThiolB@223] 203) Frac 674.817 2 2.4 10.5 6.70E−01 P06748 NPM Nucleophosmin SAPGGGSKVPQK (SEQ [ThiolB@150] ID NO: 442) Frac 767.391 1 −3.1 13.3 3.70E−01 P06748 NPM Nucleophosmin TPKGPSSVEDIK (SEQ ID [Alkene@239] NO: 329) Frac 747.345 2 −2.3 14.1 2.60E−01 P06748 NPM Nucleophosmin TPKGPSSVEDIK (SEQ ID [Thiol@239] NO: 330) Frac 656.342 2 −1.8 24.9 2.70E−05 P06748 NPM Nucleophosmin TPKGPSSVEDIK (SEQ ID [ThiolB@239] NO: 330) Frac 363.213 2 −0.7 22.0 7.80E−03 P06748 NPM Nucleophosmin TPKTPK (SEQ ID NO: [Alkene@236] 331) Fil 467.721 2 −2.7 10.0 8.30E−01 P06899 H2B1J Histone H2B type 1-J SAPAPKK (SEQ ID NO: [ThiolB@12] 325) Fil 478.261 2 4.1 14.1 8.60E−01 P06899 H2B1J Histone H2B type 1-J LAHYNKR (SEQ ID NO: [Alkene@86] 181) Frac 514.765 2 −3.1 27.5 4.20E−04 P07197 NFM Neurofilament medium SPVEEAKSK (SEQ ID [Alkene@691] polypeptide NO: 332) Frac 555.246 2 −0.5 15.6 3.10E−02 P07197 NFM Neurofilament medium SPVEEKGK (SEQ ID NO: [ThiolB@625] polypeptide 229) Frac 620.821 2 −5.8 23.4 8.20E−04 P07197 NFM Neurofilament medium SPVSKSPVEEK (SEQ ID [Alkene@671] polypeptide NO: 333) Frac 392.215 2 −2.5 16.3 4.10E−01 P07197 NFM Neurofilament medium VEKPEK (SEQ ID NO: [Alkene@609] polypeptide 334) Frac 406.728 2 −3.1 23.7 2.90E−03 P07197 NFM Neurofilament medium KAESPVK (SEQ ID NO: [ThiolB@733] polypeptide 336) Frac 590.831 2 −2.1 24.1 2.70E−04 P07197 NFM Neurofilament medium SPVKATAPEVK (SEQ ID [Alkene@514] polypeptide NO: 337) Frac 901.338 2 −2.9 26.0 1.40E−05 P07197 NFM Neurofilament medium EKAGGEGGSEEEGSDK [ThiolB@776] polypeptide (SEQ ID NO: 338) Frac 721.361 2 −1.5 12.7 1.20E−01 P07197 NFM Neurofilament medium KEDIAVNGEVEGK (SEQ [Alkene@797] polypeptide ID NO: 339) Frac 721.852 2 −2.9 42.7 1.10E−06 P07197 NFM Neurofilament medium KEDIAVNGEVEGK (SEQ [Alkene@797, Deamidated@803] polypeptide ID NO: 340) Frac 386.713 2 −1.6 28.4 2.00E−02 P07197 NFM Neurofilament medium SKAEVGK (SEQ ID NO: [Alkene@693] polypeptide 226) Frac 940.433 2 −4.1 21.9 4.30E−03 P07197 NFM Neurofilament medium GVVTNGLDLSPADEKK [Deamidated@832, ThiolB@842] polypeptide (SEQ ID NO: 219) Frac 619.825 2 4.6 15.6 2.60E−02 P07197 NFM Neurofilament medium VVVTKTVEK (SEQ ID [ThiolB@856] polypeptide NO: 235) Frac 464.242 2 −1.6 23.7 2.70E−03 P07197 NFM Neurofilament medium SPVEEKGK (SEQ ID NO: [ThiolB@625] polypeptide 229) Frac 716.837 2 −2.2 14.0 9.20E−02 P07197 NFM Neurofilament medium SPVPKSPVEEK (SEQ ID [ThiolB@619] polypeptide NO: 231) Frac 625.833 2 −3.2 9.0 2.30E+00 P07197 NFM Neurofilament medium SPVPKSPVEEK (SEQ ID [ThiolB@619] polypeptide NO: 231) Frac 884.931 2 −3.4 22.7 1.70E−03 P07197 NFM Neurofilament medium KVQSLQDEVAFLR (SEQ [ThiolB@223] polypeptide ID NO: 341) Frac 536.797 2 −1.6 25.6 8.70E−03 P07197 NFM Neurofilament medium SEEKVVVTK (SEQ ID [Alkene@851] polypeptide NO: 224) Frac 710.358 2 −1.9 36.1 1.70E−04 P07197 NFM Neurofilament medium YAKLTEAAEQNK (SEQ ID [Alkene@298] polypeptide NO: 305) Frac 1047.990 2 −5.3 52.5 1.00E−06 P07197 NFM Neurofilament medium QKQASHAQLGDAYDQEIR [Gln->pyro-Glu@138, Alkene@139] polypeptide (SEQ ID NO: 169) Frac 625.305 2 −2.5 31.8 1.90E−04 P07197 NFM Neurofilament medium SAKEEIAEYR (SEQ ID [Alkene@314] polypeptide NO: 342) Frac 469.239 3 −3.3 15.1 1.40E−01 P07197 NFM Neurofilament medium SAKEEIAEYRR (SEQ ID [Alkene@314] polypeptide NO: 343) Frac 422.246 3 −2.0 28.1 1.00E−03 P07197 NFM Neurofilament medium VEKVTSHAIVK (SEQ ID [Alkene@902] polypeptide NO: 344) Frac 864.886 2 −1.1 22.7 4.90E−04 P07197 NFM Neurofilament medium TVEKITSEGGDGATK (SEQ [ThiolB@860] polypeptide ID NO: 232) Frac 483.217 2 −5.3 15.9 5.80E−02 P07197 NFM Neurofilament medium VEKPEK (SEQ ID NO: [ThiolB@609] polypeptide 335) Frac 661.353 2 −0.8 23.4 9.80E−04 P07197 NFM Neurofilament medium SPVPKSPVEEAK (SEQ ID [Alkene@684] polypeptide NO: 345) Frac 661.351 2 −3.8 24.4 2.90E−04 P07197 NFM Neurofilament medium SPVPKSPVEEAK (SEQ ID [Alkene@684] polypeptide NO: 345) Frac 625.834 2 −1.6 26A 3 40E−03 P07197 NFM Neurofilament medium SPVPKSPVEEK (SEQ ID [Alkene@619] polypeptide NO: 230) Frac 620.824 2 −1.0 39.3 9.30E−05 P07197 NFM Neurofilament medium SPVSKSPVEEK (SEQ ID [Alkene@671] polypeptide NO: 333) Frac 620.824 2 −1.0 26.3 1.60E−04 P07197 NFM Neurofilament medium SPVSKSPVEEK (SEQ ID [Alkene@671] polypeptide NO: 333) Frac 661.370 2 −2.6 30.5 4.30E−05 P07197 NFM Neurofilament medium YITKSVTVTQK (SEQ ID [Alkene@875] polypeptide NO: 346) Frac 891.966 2 −1.4 35.8 2.00E−05 P07197 NFM Neurofilament medium VQHKFVEEIIEETK (SEQ [Alkene@451] polypeptide ID NO: 348) Frac 752.376 2 0.9 12.3 6.90E−01 P07197 NFM Neurofilament medium YITKSVTVTQK (SEQI D [ThiolB@875] polypeptide NO: 347) Frac 807.919 2 −1.6 33.9 1.60E−06 P07900 HS90A Heat shock protein HSP ELISNSSDALDKIR (SEQ [Alkene@58] 90-alpha ID NO: 349) Frac 668.826 2 −3.0 14.0 1.50E−01 P07910 HNRPC Heterogeneous nuclear LKGDDLQAIK (SEQ ID [ThiolB@189] ribonucleoproteins C1/C2 NO: 350) Frac 1452.754 1 −2.8 25.9 9.40E−03 P07910 HNRPC Heterogeneous nuclear QKVDSLLENLEK (SEQ ID [Gln->pyro-Glu@205, Alkene@206] ribonucleoproteins C1/C2 NO: 351) Frac 735.395 2 −1.3 31.9 6.00E−05 P07910 HNRPC Heterogeneous nuclear QKVDSLLENLEK (SEQ ID [Alkene@206] ribonucleoproteins C1/C2 NO: 352) Frac 652.272 2 −2.9 10.0 2.50E−02 P07910 HNRPC Heterogeneous nuclear SGFNSKSGQR (SEQ ID [ThiolB@176] ribonucleoproteins C1/C2 NO: 353) Frac 648.860 2 −2.4 32.7 6.80E−04 P08107 HSP71 Heat shock 70 kDa protein STLEPVEKALR (SEQ ID [Alkene@319] 1A/1B NO: 354) Fil, Frac, 529.278 2 −3.5 32.3 6.30E−03 P08107 HSP71 Heat shock 70 kDa protein LSKEEIER (SEQ ID NO: [Alkene@512] Lys 1A/1B 240) Frac 351.182 2 −1.4 18.0 5.30E−02 P08107 HSP71 Heat shock 70 kDa protein TGKGER (SEQ ID NO: [Alkene@190] 1A/1B 355) Frac 799.920 2 −3.6 31.5 1.40E−04 P08238 HS90B Heat shock protein HSP ELISNASDALDKIR (SEQ [Alkene@53] 90-beta ID NO: 307) Frac 1147.091 2 −3.1 22.0 3.40E−03 P08670 VIME Vimentin FLEQQNKILLAELEQLK [ThiolB@129] (SEQ ID NO: 356) Frac 692.419 2 −0.8 18.5 2.10E−02 P08670 VIME Vimentin RTLLIKTVETR (SEQ ID [Alkene@445] NO: 357) Frac 614.369 2 0.0 20.7 1.10E−02 P08670 VIME Vimentin TLLIKTVETR (SEQ ID NO: [Alkene@445] 171) Frac 885.437 2 −1.8 29.0 4.70E−05 P08670 VIME Vimentin VESLQEEIAFLKK (SEQ ID [ThiolB@235] NO: 358) Frac 821.405 2 −3.1 45.2 3.30E−05 P08670 VIME Vimentin TNEKVELQELNDR (SEQ [Alkene@104] ID NO: 303) Frac 714.377 1 −1.5 7.8 1.60E−01 P0C0S5 H2AZ Histone H2A.Z GQQKTV (SEQ ID NO: [Alkene@126] 359) Frac 714.377 2 −1.5 7.8 1.00E−01 POCOS5 H2AZ Histone H2A.Z KGQQK (SEQ ID NO: [Alkene@122] 360) Frac 657.886 2 1.5 16.9 8.50E−03 P10412 H14 Histone H1.4 SLVSKGTLVQTK (SEQ ID [Alkene@90] NO: 361) Fil 348.706 2 1.2 18.5 1.80E−02 P10412 H14 Histone H1.4 KPAGAAK (SEQ ID NO: [Alkene@130] 362) Fil 363.250 2 1.0 19.9 1.30E−02 P10412 H14 Histone H1.4 IKLGLK (SEQ ID NO: [Alkene@81] 363) Frac 363.249 2 −1.7 16.5 3.10E−02 P10412 H14 Histone H1.4 IKLGLK (SEQ ID NO: [Alkene@81] 363) Frac 499.814 2 −3.7 32.5 2.10E−04 P10412 H14 Histone H1.4 LGLKSLVSK (SEQ ID [Alkene@85] NO: 364) Frac 657.883 2 −3.1 9.0 7.40E−01 P10412 H14 Histone H1.4 SLVSKGTLVQTK (SEQ ID [Alkene@90] NO: 361) Lys 404.701 2 0.5 8.9 9.20E−01 P10412 H14 Histone H1.4 TPVKK (SEQ ID NO: [ThiolB@21] 365) Fil 884.018 2 5.1 24.9 2.10E−03 P10809 CH60 60 kDa heat shock protein, RGVMLAVDAVIAELKK [Alkene@156] mitochondrial (SEQ ID NO: 366) Fil 424.237 2 −0.6 22.9 1.10E−01 P10809 CH60 60 kDa heat shock protein, YKNIGAK (SEQ ID NO: [Alkene@91] mitochondrial 367) Frac, Lys 390.690 2 −2.0 8.4 5.30E+00 P12277 KCRB Creatine kinase B-type LQKR (SEQ ID NO: [ThiolB@319] 368) Lys 513.315 2 −1.4 30.7 7.90E−03 P13639 EF2 Elongation factor 2 LIEKLDIK (SEQ ID NO: [Alkene@318] 369) Fil 527.320 2 2.3 18.9 2.80E−03 P14314 GLU2B Glucosidase 2 subunit beta KLIELQAGK (SEQ ID [Alkene@158] NO: 370) Fil 363.250 2 1.0 19.9 1.30E−02 P16403 H12 Histone H1.2 IKLGLK (SEQ ID NO: [Alkene@81] 363) Frac 1078.015 2 −8.5 29.9 1.30E−04 P19338 NUCL Nucleolin TGISDVFAKNDLAVVDVR [ThiolB@333] (SEQ ID NO: 371) Frac 607.859 2 −3.0 34.9 1.50E−04 P19338 NUCL Nucleolin TLLAKNLPYK (SEQ ID [Alkene@398] NO: 372) Frac 469.786 2 −2.4 25.9 1.00E−04 P19338 NUCL Nucleolin KVAVATPAK (SEQ ID [Alkene@71] NO: 373) Frac, Lys 607.860 2 −1.3 23.0 4.60E−04 P19338 NUCL Nucleolin TLLAKNLPYK (SEQ ID [Alkene@398] NO: 372) Frac 606.844 2 −2.2 19.6 9.60E−04 P20700 LMNB1 Lamin-B1 KQLADETLLK (SEQ ID [Alkene@182] NO: 374) Frac 832.906 2 −4.5 19.6 1.80E−02 P20700 LMNB1 Lamin-B1 IQELEDLLAKEK (SEQ ID [ThiolB@330] NO: 375) Frac 812.935 2 −1.6 37.7 1.30E−05 P20700 LMNB1 Lamin-B1 VILKNSQGEEVAQR (SEQ [Alkene@532] ID NO: 376) Lys 478.261 2 4.1 14.1 8.60E−01 P23527 H2B10 Histone H2B type 1-O LAHYNKR (SEQ ID NO: [Alkene@86] 181) Lys 1465.693 2 −0.8 15.4 8.60E−02 P23527 H2B10 Histone H2B type 1-O QVHPDTGISSKAMGIMNSF [Gln->pyro-Glu@48, Alkene@58] VNDIFER (SEQ ID NO: 377) Frac 510.770 2 −3.2 22.0 1.70E−02 P24534 EF1B Elongation factor 1-beta LAQYESKK (SEQ ID NO: [ThiolB@129] 378) Lys 651.342 3 −0.5 22.9 1.80E−02 P27824 CALX Calnexin LLSKTPELNLDQFHDK [Alkene@170] (SEQ ID NO: 379) Fil 611.845 2 3.0 25.5 1.60E−03 P30101 PDIA3 Protein disulfide- TADGIVSHLKK (SEQ ID [Alkene@129] isomerase A3 NO: 380) Fil 728.387 2 3.0 30.7 1.70E−04 P51572 BAP31 B-cell receptor-associated LEKAENQVLAMR (SEQ [Alkene@204] protein 31 ID NO: 381) Frac 662.881 2 −2.7 12.8 6.80E−01 P52272 HNRPM Heterogeneous nuclear INEILSNALKR (SEQ ID [Alkene@381] ribonucleoprotein M NO: 382) Frac 913.948 2 −1.5 14.5 2.50E−01 P61353 RL27 60S ribosomal protein L27 YSVDIPLDKTVVNK (SEQ [ThiolB@93] ID NO: 383) Frac 822.945 2 −1.0 18.7 1.90E−03 P61353 RL27 60S ribosomal protein L27 YSVDIPLDKTVVNK (SEQ [Alkene@93] ID NO: 384) Fil 626.848 2 −0.7 27.6 2.30E−05 P61604 CH10 10 kDa heat shock protein, GKGGEIQPVSVK (SEQ ID [Alkene@56] mitochondrial NO: 270) Frac, Lys 356.228 2 −3.5 11.6 8.40E−01 P61978 HNRPK Heterogeneous nuclear IKQIR (SEQ ID NO: [Alkene@411] ribonucleoprotein K 385) Frac 356.228 2 −3.5 16.8 2.90E−01 P61978 HNRPK Heterogeneous nuclear IKQIR (SEQ ID NO: [Alkene@411] ribonucleoprotein K 385) Fil, Frac, 335.697 2 −2.3 21.5 5.30E−02 P62805 H4 Histone H4 GGKGLGK (SEQ ID NO: [Alkene@9] Lys 159) Frac, Lys 371.217 2 1.8 21.9 1.90E−02 P62805 H4 Histone H4 GLGKGGAK (SEQ ID [Alkene@13] NO: 162) Frac 811.933 2 −3.5 22.5 1.00E−01 P62805 H4 Histone H4 GVLKVFLENVIR (SEQ ID [ThiolB@60] NO: 386) Frac 573.809 2 −4.0 24.8 5.40E−05 P62807 H2B1C Histone H2B type 1- MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] C/E/F/G/I ID NO: 301) Frac 573.808 2 −5.8 21.4 1.20E−03 P62807 H2B1C Histone H2B type 1- MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] C/E/F/G/I ID NO: 301) Frac 467.721 2 −2.7 10.0 8.30E−01 P62807 H2B1C Histone H2B type 1- SAPAPKK (SEQ ID NO: [ThiolB@12] C/E/F/G/I 325) Frac 454.216 2 −2.3 26.2 6.80E−03 P20671 H2A1D Histone H2A type 1-D KGNYSER (SEQ ID NO: [Alkene@37] 158) Fil, Frac 478.258 2 −2.2 26.6 1.30E−02 P62807 H2B1C Histone H2B type 1- LAHYNKR (SEQ ID NO: [Alkene@86] C/E/F/G/I 181) Frac 1465.693 2 −0.8 28.1 2.90E−04 P62807 H2B1C Histone H2B type 1- QVHPDTGISSKAMGIMNSF [Gln->pyro-Glu@48, Alkene@58] C/E/F/G/I VNDIFER (SEQ ID NO: 377) Fil 781.896 2 −0.1 17.3 1.90E−01 P62807 H2B1C Histone H2B type 1- SRKESYSVYVYK (SEQ ID [Alkene@35] C/E/F/G/I NO: 297) Lys 559.308 4 1.0 33.5 2.40E−03 P62826 RAN GTP-binding nuclear KYVATLGVEVHPLVFHTNR [Alkene@38] protein Ran (SEQ ID NO: 387) Fil, Lys 550.764 2 −1.8 23.7 3.20E−04 P62841 RS15 40S ribosomal protein S15 QHSLLKR (SEQ ID NO: [Gln->pyro-Glu@53, ThiolB@58] 388) Lys 558.295 2 −1.5 30.9 6.90E−05 P62937 PPIA Peptidyl-prolyl cis-trans VPKTAENFR (SEQ ID [Alkene@31] isomerase A NO: 390) Frac 564.810 2 −1.7 36.8 6.30E−04 Q00839 HNRPU Heterogeneous nuclear VSELKEELK (SEQ ID [Alkene@17] ribonucleoprotein U NO: 391) Fil, Frac 531.938 3 −1.6 22.6 3.00E−03 Q00839 HNRPU Heterogeneous nuclear TTWVTKHAAENPGK [Alkene@516] ribonucleoprotein U (SEQ ID NO: 392) Frac 727.428 2 −2.6 28.6 2.70E−04 Q02878 RL6 60S ribosomal protein L6 IKAIPQLQGYLR (SEQ ID [Alkene@262] NO: 393) Frac 442.699 2 −2.1 9.3 3.30E−01 Q14103 HNRPD Heterogeneous nuclear IMEKK (SEQ ID NO: [ThiolB@242] ribonucleoprotein D0 394) Frac 789.885 2 −1.7 18.2 8.80E−04 Q15149 PLEC Plectin TPVEVPVGGFKGR (SEQ [Alkene@3384] ID NO: 395) Frac 586.798 2 −1.6 26.6 2.00E−02 Q15149 PLEC Plectin SAEAELQSKR (SEQ ID [Alkene@1718] NO: 396) Frac 920.918 2 −1.6 25.5 9.90E−04 Q15149 PLEC Plectin QLAEAHAQAKAQAER [Gln->pyro-Glu@1511, ThiolB@1520] (SEQ ID NO: 397) Frac 819.380 2 1.1 14.6 2.20E−01 Q15149 PLEC Plectin VQKSLAAEEEAAR (SEQ [ThiolB@2129] ID NO: 398) Frac 328.197 2 −2.8 13.8 3.90E−01 Q15233 NONO Non-POU domain- GKQLR (SEQ ID NO: [Alkene@137] containing octamer- 399) binding protein Frac 573.809 2 −4.0 24.8 5.40E−05 Q16778 H2B2E Histone H2B type 2-E MPEPAKSAPAPK (SEQ [Met-loss@1, Alkene@6] ID NO: 301) Fil, Frac 478.261 2 4.1 14.1 8.60E−01 Q16778 H2B2E Histone H2B type 2-E LAHYNKR (SEQ ID NO: [ThiolB@86] 400) Frac 485.756 2 −1.8 21.3 3.00E−01 Q6FI13 H2A2A Histone H2A type 2-A MSGRGKQGGK (SEQ ID [Met-loss + Acetyl@1, Alkene@6] NO: 401) Frac 499.292 2 −2.2 19.3 1.40E−01 Q71DI3 H32 Histone H3.2 KSTGGKAPR (SEQ ID [TriMethyl@10 = 27, Alkene@15 = 27] NO: 402) Lys 492.284 2 −2.6 20.9 5.40E−02 Q71DI3 H32 Histone H3.2 KSTGGKAPR (SEQ ID [Dimethyl@10 = 35, Alkene@15 = 35] NO: 403) Fil, Frac, 379.711 2 22.3 2.70E−02 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] Lys 294) Frac 743.867 2 −0.9 16.1 1.20E−01 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [ThiolB@57] NO: 311) Frac 492.285 2 −0.5 19.6 1.20E−01 Q71DI3 H32 Histone H3.2 KSTGGKAPR (SEQ ID [Dimethyl@10 = 24, Alkene@15 = 24] NO: 404) Frac 499.274 2 −1.8 25.7 1.00E−03 Q71DI3 H32 Histone H3.2 KSTGGKAPR (SEQ ID [Acetyl@10&Alkene@15|Acetyl@15 NO: 405) &Alkene@10] Frac, Lys 379.711 2 −1.1 22.4 3.70E−01 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [Alkene@5] 294) Fil 895.502 1 2.7 12.7 8.10E−02 Q71DI3 H32 Histone H3.2 QLATKAAR (SEQ ID [Gln->pyro-Glu@20, Alkene@24] NO: 406) Frac 470.718 2 6.4 11.7 2.60E−01 Q71DI3 H32 Histone H3.2 TKQTAR (SEQ ID NO: [ThiolB@5] 295) Frac 719.905 2 −4.1 12.8 2.50E−01 Q71DI3 H32 Histone H3.2 VTIMPKDIQLAR (SEQ ID [Alkene@123] NO: 312) Frac 652.861 2 −4.7 25.7 2.30E−03 Q71DI3 H32 Histone H3.2 YQKSTELLIR (SEQ ID [Alkene@57] NO: 310) Lys 467.721 2 −2.7 10.0 8.30E−01 Q93079 H2B1H Histone H2B type 1-H SAPAPKK (SEQ ID NO: [ThiolB@12] 325) Fil 467.721 2 −2.7 10.0 8.30E−01 Q99877 H2B1N Histone H2B type 1-N SAPAPKK (SEQ ID NO: [ThiolB@12] 325) Fil 781.896 2 −0.1 17.3 1.90E−01 Q99877 H2B1N Histone H2B type 1-N SRKESYSVYVYK (SEQ ID [Alkene@35] NO: 297) Frac 568.240 2 −2.7 14.0 4.20E−03 Q9NVA2 SEPT11 Septin-11 THQEEKK (SEQ ID NO: [ThiolB@378] 407)

TABLE 11 Subunit ACC# Protein Name K-K linkage Sites Bait P25789-P62195 alpha3:Rpt6 alpha-3:K210-Rpt6:K402 Rpt6 P25789-P62195 alpha3-Rpt6 alpha3:K205-Rpt6:K330 Rpt6 P25789-P62195 alpha3-Rpt6 alpha3:K210-Rpt6:K393 Rpt6 O00487-P62195 Rpn11-Rpt6 Rpn11:K277-Rpt6:K55 Rpn11 P62195-Q99460 Rpn2-Rpt6 Rpn2:K720-Rpt6:K82 Rpt6 O00231-O00232 Rpn5-Rpn6 Rpn5:K207-Rpn6:K295 Rpn11 O00232-Q9UNM6 Rpn5-Rpn9 Rpn5:K368-Rpn9:K321 Rpn11 P62191-P62195 Rpt2-Rpt6 Rpt2:K258-Rpt6:K222 Rpt6 P43686-P62195 Rpt3-Rpt6 Rpt3:K238-Rpt6:K222 Rpt6 P43686-P62195 Rpt3-Rpt6 Rpt3:K80-Rpt6:K55 Rpt6 P62195-P62333 Rpt4:Rpt6 Rpt4:K72-Rpt6:K222 Rpt6 P08107-P11142 HSPA1A- HSPA1A:K512- Rpn11 HSPA8 HSPA8:K507 [P25789] alpha-3 K231-K239 Rpt6 [O00487] Rpn11 K257-K273 Rpn11 [O00487] Rpn11 K257-K277 Rpn11 [P17980] Rpt5 K70-K74 Rpt6 [P62195] Rpt6 K330-K335 Rpt6 [P62195] Rpt6 K393-K402 Rpt6 [P62195] Rpt6 K55-K82 Rpt6 [P62195] Rpt6 K82-K84 Rpt6 [P62195] Rpt6 K84-K94 Rpt6 [P62195] Rpt6 K88-K222 Rpt6 [P62195] Rpt6 K94-K222 Rpt6 [P13639] EEF2 K239-K318 Rpt6 [P13639] EEF2 K252-K259 Rpt6 [P08107] HSPA1A K507-K512 Rpt6 [P62841] RPS15 K58-K65 Rpn11

TABLE 12 MS1 m/z MS1 z ppm P1 m/z P1 z P1 ppm P1 score P1 ev P1 ACC P1 protein P1 peptide P1 mod 571.7661 4 0.059 719.858 2 0.5 15.4 2.10E−02 Q99460 Rpn2 VINDKHDDVMAK (SEQ ID NO: 408) XL:B-Alkene@720 540.2740 4 1.989 436.266 2 0.0 15.9 1.60E−01 O00232 Rpn5 TQIISKK (SEQ ID NO: 409) XL:B-Alkene@207 746.3817 4 0.305 550.286 2 3.9 24.7 9.10E−04 O00232 Rpn5 IMAKYYTR (SEQ ID NO: 410) XL:B-Alkene@368 534.7686 4 1.794 470.249 2 1.4 19 1.10E−02 O00487 Rpn11 NVGKQDPK (SEQ ID NO: 411) XL:B-Alkene@277 922.4770 4 9.846 878.969 2 −9.8 23.3 3.60E−03 P62191 Rpt2 WGSELIQKYLGDGPK (SEQ ID NO: 412) XL:B-Alkene@258 659.8259 4 2.235 720.366 2 −0.7 26 1.60E−04 P43686 Rpt3 EFLHAQEEVKR (SEQ ID NO: 413) XL:B-Alkene@80 937.9707 4 0.243 909.974 2 1.2 27.4 1.70E−03 P43686 Rpt3 WGSEFVQKYLGEGPR (SEQ ID NO: 414) XL:B-Alkene@238 772.3973 4 1.131 578.828 2 −0.5 31.7 7.30E−05 P62333 Rpt4 FIVKATNGPR (SEQ ID NO: 415) XL:B-Alkene@72 653.3353 4 0.571 574.845 2 0.1 21 6.40E−03 P62195 Rpt6 LDILKIHSR (SEQ ID NO: 416) XL:B-Alkene@330 676.3400 4 0.211 509.748 2 1.3 26.2 3.10E−03 P62195 Rpt6 VMQKDSEK (SEQ ID NO: 417) XL:B-Alkene@393 615.3207 4 0.094 478.715 2 −2.4 13.3 5.70E−01 P62195 Rpt6 NMSIKK (SEQ ID NO: 418) XL:B-Thiol@402 820.0922 3 0.769 774.417 1 −1.1 14.4 8.60E−01 P62195 Rpt6 NMSIKK (SEQ ID NO: 419) XL:B-Alkene@402 582.7930 4 1.964 529.282 2 0.0 24.5 3.60E−03 P08107 HSP1A/B LSKEEIER (SEQ ID NO: 240) XL:B-Alkene@512 769.3677 4 0.260 696.824 2 5.0 25.8 1.30E−03 O00487 Rpn11 NYNKAVEEEDK (SEQ ID NO: 420) XL:B-Alkene@257 633.5399 4 0.383 696.819 2 2.1 25.2 1.30E−03 O00487 Rpn11 NYNKAVEEEDK (SEQ ID NO: 420) XL:B-Alkene@257 614.2955 4 0.583 677.346 2 0.0 31 2.20E−05 P17980 Rpt5 VTHELQAMKDK (SEQ ID NO: 421) XL:B-Alkene@70 461.4756 4 0.470 499.276 2 0.0 21.4 9.00E−03 P62195 Rpt6 NELNAKVR (SEQ ID NO: 422) XL:B-Alkene@55 495.9291 3 0.855 414.669 2 0.0 8.5 5.20E−01 P62195 Rpt6 AMDKK (SEQ ID NO: 423) XL:B-Thiol@82 591.3166 4 2.046 640.440 1 0.0 8.1 7.10E−01 P62195 Rpt6 KVLVK (SEQ ID NO: 425) XL:B-Alkene@84 773.1585 4 2.684 580.346 2 1.7 29.8 3.20E−05 P62195 Rpt6 VLVKVHPEGK (SEQ ID NO: 426) XL:B-Alkene@88 863.9333 4 1.921 761.901 2 1.8 24.4 3.10E−04 P62195 Rpt6 VHPEGKFVVDVDK (SEQ ID NO: 427) XL:B-Alkene@94 541.7886 4 0.846 574.843 2 0.0 32.2 6.70E−05 P62195 Rpt6 LDILKIHSR (SEQ ID NO: 416) XL:B-Alkene@330 664.6444 3 0.819 509.748 2 0.0 24.1 8.40E−03 P62195 Rpt6 VMQKDSEK (SEQ ID NO: 417) XL:B-Alkene@393 601.7863 4 3.899 527.246 2 0.0 22.6 2.40E−03 P25789 α3 KHEEEEAK (SEQ ID NO: 428) XL:B-Alkene@239 678.1033 4 6.140 742.878 2 0.0 22.9 2.60E−02 P13639 EEF2 FAAKGEGQLGPAER (SEQ ID NO: 253) XL:B-Alkene@239 491.2270 4 1.168 558.724 2 0.0 17.3 5.00E−04 P13639 EEF2 KVEDMMK (SEQ ID NO: 429) XL:B-Thiol@252 582.7930 4 1.964 536.290 2 0.0 25.7 6.30E−03 P08107 HSP1A/1B ITITNDKGR (SEQ ID NO: 239) XL:B-Alkene@507 531.6768 5 −2.563 459.763 2 0.0 19.6 4.00E−03 P62841 RPS15 QHSLLKR (SEQ ID NO: 389) XL:B-Alkene@58 P2 P2 m/z P2 z P2 ppm P2 score P2 ev P2 ACC protein P2 peptide P2 mod linkage lysine-lysine linkage Bait 646.323 1 0.2 7.4 5.70E−01 P62195 Rpt6 AMDKK (SEQ ID NO: 424) XL:B-Alkene@82 Rpn2:Rpt6 Rpn2-K720:Rpt6-K82 Rpt6 544.271 2 3.1 20.9 7.70E−03 O00231 Rpn6 CVAQASKNR (SEQ ID NO: 430) XL:B-Alkene@295 Rpn5:Rpn6 Rpn5-K207:Rpn6-K295 Rpn11 842.469 2 8.5 14.8 2.80E−02 Q9UNM6 Rpn9 ALSVGLVKGSIDEVDK (SEQ ID NO: 431) XL:B-Alkene@321 Rpn5:Rpn9 Rpn5-K368:Rpn9-K321 Rpn11 499.276 2 2.2 27.7 3.40E−03 P62195 Rpt6 NELNAKVR (SEQ ID NO: 422) XL:B-Alkene@55 Rpn11:Rpt6 Rpn11-K277:Rpt6-K55 Rpn11 865.958 2 0.9 31.3 5.60E−04 P62195 Rpt6 VSGSELVQKFIGEGAR (SEQ ID NO: 432) XL:B-Alkene@222 Rpt2:Rpt6 Rpt2-K258:Rpt6-K222 Rpt6 499.274 2 0.2 27.6 3.20E−03 P62195 Rpt6 NELNAKVR (SEQ ID NO: 422) XL:B-Alkene@55 Rpt3:Rpt6 Rpt3-K80:Rpt6-K55 Rpt6 865.959 2 0.9 29.6 1.10E−03 P62195 Rpt6 VSGSELVQKFIGEGAR (SEQ ID NO: 432) XL:B-Alkene@222 Rpt3:Rpt6 Rpt3-K238:Rpt6-K222 Rpt6 865.956 2 0.9 31.5 4.00E−04 P62195 Rpt6 VSGSELVQKFIGEGAR (SEQ ID NO: 432) XL:B-Alkene@222 Rpt4:Rpt6 Rpt4-K72:Rpt6-K222 Rpt6 631.816 2 −3.9 22.4 2.50E−03 P25789 α3 TMDVSKLSAEK (SEQ ID NO: 434) XL:B-Alkene@205 Rpt6:α3 Rpt6-K330:α3-K205 Rpt6 742.922 2 0.6 23.7 1.10E−03 P25789 α3 LSAEKVEIATLTR (SEQ ID NO: 435) XL:B-Alkene@210 Rpt6:α3 Rpt6-K393:α3-K210 Rpt6 742.921 2 0.6 29.4 1.40E−04 P25789 α3 LSAEKVEIATLTR (SEQ ID NO: 435) XL:B-Alkene@210 Rpt6:α3 Rpt6-K402:α3-K210 Rpt6 742.920 2 0.6 37.3 5.50E−05 P25789 α3 LSAEKVEIATLTR (SEQ ID NO: 435) XL:B-Alkene@210 Rpt6:α3 Rpt6-K402:α3-K210 Rpt6 536.29 2 0.0 20.6 2.10E−02 P11142 HSPA8 ITITNDKGR (SEQ ID NO: 239) XL:B-Alkene@507 HSPA1A/ HSP1A/B-K512:HSPA8-K507 Rpn11 B:HSPA8* 741.910 2 0.2 20 7.90E−03 O00487 Rpn11 MTPEQLAIKNVGK (SEQ ID NO: 436) XL:B-Alkene@273 Rpn11 Rpn11-K257:Rpn11-K273 Rpn11 470.250 2 3.5 16.6 4.20E−02 O00487 Rpn11 NVGKQDPK (SEQ ID NO: 411) XL:B-Alkene@277 Rpn11 Rpn11-K257:Rpn11-K277 Rpn11 451.235 2 0.0 20.8 6.70E−03 P17980 Rpt5 IKENSEK (SEQ ID NO: 437) XL:B-Alkene@74 Rpt5 Rpt5-K70:Rpt5-K74 Rpt6 646.324 1 0.0 8.9 4.80E−01 P62195 Rpt6 AMDKK (SEQ ID NO: 424) XL:B-Alkene@82 Rpt6 Rpt6-K55:Rpt6-K82 Rpt6 640.440 1 0.0 12.6 1.60E−01 P62195 Rpt6 KVLVK (SEQ ID NO: 425) XL:B-Alkene@84 Rpt6 Rpt6-K82:Rpt6-K84 Rpt6 568.937 3 0.0 26.6 1.00E−04 P62195 Rpt6 VHPEGKFVVDVDK (SEQ ID NO: 427) XL:B-Alkene@94 Rpt6 Rpt6-K84:Rpt6-K94 Rpt6 865.958 2 0.9 16.6 6.30E−02 P62195 Rpt6 VSGSELVQKFIGEGAR (SEQ ID NO: 432) XL:B-Alkene@222 Rpt6 Rpt6-K88:Rpt6-K222 Rpt6 956.957 2 −4.0 22.8 1.10E−02 P62195 Rpt6 VSGSELVQKFIGEGAR (SEQ ID NO: 433) XL:B-Thiol@222 Rpt6 Rpt6-K94:Rpt6-K222 Rpt6 408.724 2 0.0 21.6 1.40E−01 P62195 Rpt6 KMNLTR (SEQ ID NO: 438) XL:B-Alkene@335 Rpt6 Rpt6-K330:Rpt6-K335 Rpt6 774.419 1 0.0 13.1 1.60E−01 P62195 Rpt6 NMSIKK (SEQ ID NO: 419) XL:B-Alkene@402 Rpt6 Rpt6-K393:Rpt6-K402 Rpt6 576.323 2 0.0 18.3 3.30E−02 P25789 α3 QKEVEQLIK (SEQ ID NO: 439) XL:B-Alkene@231 α3 α3-K239:α3-K231 Rpt6 513.315 2 0.0 20.6 1.60E−02 P13639 EEF2 LIEKLDIK (SEQ ID NO: 369) XL:B-Alkene@318 EEF2 EEF2-K239:EEF2-K318 Rpt6 414.723 2 0.0 19.9 6.10E−03 P13639 EEF2 KLWGDR (SEQ ID NO: 440) XL:B-Alkene@259 EEF2 EEF2-K252:EEF2-K259 Rpt6 529.282 2 0.0 26 1.10E−02 P08107 HSP1A/B LSKEEIER (SEQ ID NO: 240) XL:B-Alkene@512 HSPA1A/1B HSP1A/B-K507:HSP1A/B-K512 Rpt6 512.611 3 0.0 18.7 8.10E−03 P62841 RPS15 KEAPPMEKPEWK (SEQ ID NO: 277) XL:B-Alkene@65 RPS15 RPS15-K58:RPS15-K65 Rpn11 Note: *since the identical sequence (ITINDKGR) present in both HSP1A and HSP8A, this identification could also present the inter-linked peptide within HSP1A protein.

DETAILED DESCRIPTION Mass Spectrometry-Cleavable Cross-Linking Agents to Facilitate Structural Analysis of Proteins and Protein Complexes, and Method of Using Same

Proteins form stable and dynamic multi-subunit complexes under different physiological conditions to maintain cell viability and normal cell homeostasis. Detailed knowledge of protein interactions and protein complex structures is fundamental to understanding how individual proteins function within a complex and how the complex functions as a whole. However, structural elucidation of large multi-subunit protein complexes has been difficult due to lack of technologies which can effectively handle their dynamic and heterogeneous nature. Traditional methods such as nuclear magnetic resonance (NMR) analysis and X-ray crystallography can yield detailed information on protein structures. However, NMR spectroscopy requires large quantities of pure protein in a specific solvent while X-ray crystallography is often limited by the crystallization process.

In recent years, chemical cross-linking coupled with mass spectrometry (MS) has become a powerful method for studying protein interactions. See for example the disclosures of Sinz, A. (2003) Chemical Cross-Linking and Mass Spectrometry for Mapping Three-Dimensional Structures of Proteins and Protein Complexes. J Mass Spectrom. 38, 1225-1237; Sinz, A. (2006) Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom Rev 25, 663-682; and Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., and Aebersold, R. (2010) Probing Native Protein Structures by Chemical Cross-Linking, Mass Spectrometry and Bioinformatics. Molecular & Cellular Proteomics 9, 1634-1649.

Chemical cross-linking stabilizes protein interactions through the formation of covalent bonds and allows the detection of stable, weak and/or transient protein-protein interactions in native cells or tissues See for example the disclosures of Sinz, A. (2010) Investigation of Protein-Protein Interactions in Living Cells by Chemical Cros slinking and Mass Spectrometry. Anal Bioanal Chem 397, 3433-3440; Vasilescu, J., Guo, X., and Kast, J. (2004) Identification of Protein-Protein Interactions Using in Vivo Cross-Linking and Mass Spectrometry. Proteomics 4, 3845-3854; Guerrero, C., Tagwerker, C., Kaiser, P., and Huang, L. (2006) An Integrated Mass Spectrometry-Based Proteomic Approach: Quantitative Analysis of Tandem Affinity-Purified in Vivo Cross-Linked Protein Complexes (Qtax) to Decipher the 26 S Proteasome-Interacting Network. Mol Cell Proteomics 5, 366-378; Tagwerker, C., Flick, K., Cui, M., Guerrero, C., Dou, Y., Auer, B., Baldi, P., Huang, L., and Kaiser, P. (2006) A Tandem Affinity Tag for Two-Step Purification under Fully Denaturing Conditions: Application in Ubiquitin Profiling and Protein Complex Identification Combined with in Vivocross-Linking. Mol Cell Proteomics 5, 737-748; Guerrero, C., Milenkovic, T., Przulj, N., Kaiser, P., and Huang, L. (2008) Characterization of the Proteasome Interaction Network Using a Qtax-Based Tag-Team Strategy and Protein Interaction Network Analysis. Proc Natl Acad Sci USA 105, 13333-13338; and Kaake, R. M., Milenkovic, T., Przulj, N., Kaiser, P., and Huang, L. (2010) Characterization of Cell Cycle Specific Protein Interaction Networks of the Yeast 26s Proteasome Complex by the Qtax Strategy. J Proteome Res 9, 2016-2019.

In addition to capturing protein interacting partners, many studies have shown that chemical cross-linking can yield low-resolution structural information about the constraints within a molecule. See for example the disclosures of Sinz, A. (2006) Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom Rev 25, 663-682; Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., and Aebersold, R. (2010) Probing Native Protein Structures by Chemical Cross-Linking, Mass Spectrometry and Bioinformatics. Molecular & Cellular Proteomics 9, 1634-1649; and Back, J. W., de Jong, L., Muijsers, A. O., and de Koster, C. G. (2003) Chemical Cross-Linking and Mass Spectrometry for Protein Structural Modeling. J Mol Biol. 331, 303-313, or protein complex, as disclosed in Rappsilber, J., Siniossoglou, S., Hurt, E. C., and Mann, M. (2000) A Generic Strategy to Analyze the Spatial Organization of Multi-Protein Complexes by Cross-Linking and Mass Spectrometry. Anal Chem. 72, 267-275; Maiolica, A., Cittaro, D., Borsotti, D., Sennels, L., Ciferri, C., Tarricone, C., Musacchio, A., and Rappsilber, J. (2007) Structural Analysis of Multiprotein Complexes by Cross-Linking, Mass Spectrometry, and Database Searching. Mol Cell Proteomics 6, 2200-2211; and Chen, Z. A., Jawhari, A., Fischer, L., Buchen, C., Tahir, S., Kamenski, T., Rasmussen, M., Lariviere, L., Bukowski-Wills, J. C., Nilges, M., Cramer, P., and Rappsilber, J. (2010) Architecture of the Rna Polymerase Ii-Tfiif Complex Revealed by Cross-Linking and Mass Spectrometry. Embo J 29, 717-726.

The application of chemical cross-linking, enzymatic digestion, and subsequent mass spectrometric and computational analysis for the elucidation of three dimensional protein structures offers distinct advantages over traditional methods due to its speed, sensitivity, and versatility. Identification of cross-linked peptides provides distance constraints that aid in constructing the structural topology of proteins and/or protein complexes.

Although this approach has been successful, effective detection and accurate identification of cross-linked peptides as well as unambiguous assignment of cross-linked sites remain extremely challenging due to their low abundance and complicated fragmentation behavior in MS analysis. See for the example the disclosures of Sinz, A. (2006) Chemical Cross-Linking and Mass Spectrometry to Map Three-Dimensional Protein Structures and Protein-Protein Interactions. Mass Spectrom Rev 25, 663-682; Leitner, A., Walzthoeni, T., Kahraman, A., Herzog, F., Rinner, O., Beck, M., and Aebersold, R. (2010) Probing Native Protein Structures by Chemical Cross-Linking, Mass Spectrometry and Bioinformatics. Molecular & Cellular Proteomics 9, 1634-1649; Back, J. W., de Jong, L., Muijsers, A. O., and de Koster, C. G. (2003) Chemical Cross-Linking and Mass Spectrometry for Protein Structural Modeling. J Mol Biol. 331, 303-313; and Schilling, B., Row, R. H., Gibson, B. W., Guo, X., and Young, M. M. (2003) Ms2assign, Automated Assignment and Nomenclature of Tandem Mass Spectra of Chemically Crosslinked Peptides. J Am Soc Mass Spectrom. 14, 834-850.

Therefore, new reagents and methods are urgently needed to allow unambiguous identification of cross-linked products and to improve the speed and accuracy of data analysis to facilitate its application in structural elucidation of large protein complexes.

A number of approaches have been developed to facilitate MS detection of low abundance cross-linked peptides from complex mixtures. These include selective enrichment using affinity purification with biotinylated cross-linkers, for example, as described in Trester-Zedlitz, M., Kamada, K., Burley, S. K., Fenyo, D., Chait, B. T., and Muir, T. W. (2003) A Modular Cross-Linking Approach for Exploring Protein Interactions. J Am Chem Soc. 125, 2416-2425; Tang, X., Munske, G. R., Siems, W. F., and Bruce, J. E. (2005) Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein-Protein Interactions. Anal Chem 77, 311-318; and Chu, F., Mahrus, S., Craik, C. S., and Burlingame, A. L. (2006) Isotope-Coded and Affinity-Tagged Cross-Linking (Icatxl): An Efficient Strategy to Probe Protein Interaction Surfaces. J Am Chem Soc 128, 10362-10363, and click chemistry with alkyne-tagged (Chowdhury, S. M., Du, X., Tolic, N., Wu, S., Moore, R. J., Mayer, M. U., Smith, R. D., and Adkins, J. N. (2009) Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry. Anal Chem 81, 5524-5532) or azide tagged cross-linkers, see for example Kasper, P. T., Back, J. W., Vitale, M., Hartog, A. F., Roseboom, W., de Koning, L. J., van Maarseveen, J. H., Muijsers, A. O., de Koster, C. G., and de Jong, L. (2007) An Aptly Positioned Azido Group in the Spacer of a Protein Cross-Linker for Facile Mapping of Lysines in Close Proximity. Chembiochem 8, 1281-1292; and Nessen, M. A., Kramer, G., Back, J., Baskin, J. M., Smeenk, L. E., de Koning, L. J., van Maarseveen, J. H., de Jong, L., Bertozzi, C. R., Hiemstra, H., and de Koster, C. G. (2009) Selective Enrichment of Azide-Containing Peptides from Complex Mixtures. J Proteome Res 8, 3702-3711.

In addition, Staudinger ligation has recently been shown to be effective for selective enrichment of azide-tagged cross-linked peptides (Vellucci, D., Kao, A., Kaake, R. M., Rychnovsky, S. D., and Huang, L. (2010) Selective Enrichment and Identification of Azide-Tagged Cross-Linked Peptides Using Chemical Ligation and Mass Spectrometry. J Am Soc Mass Spectrom 21, 1432-1445).

Apart from enrichment, detection of cross-linked peptides can be achieved by isotope-labeled, as described in Collins, C. J., Schilling, B., Young, M., Dollinger, G., and Guy, R. K. (2003) Isotopically Labeled Crosslinking Reagents: Resolution of Mass Degeneracy in the Identification of Crosslinked Peptides. Bioorg Med Chem Lett. 13, 4023-4026; Petrotchenko, E. V., Olkhovik, V. K., and Borchers, C. H. (2005) Isotopically Coded Cleavable Cross-Linker for Studying Protein-Protein Interaction and Protein Complexes. Mol Cell Proteomics 4, 1167-1179; and Petrotchenko, E., and Borchers, C. (2010) Icc-Class: Isotopically-Coded Cleavable Crosslinking Analysis Software Suite. BMC bioinformatics 11, 64, fluorescently labeled (Sinz, A., and Wang, K. (2004) Mapping Spatial Proximities of Sulfhydryl Groups in Proteins Using a Fluorogenic Cross-Linker and Mass Spectrometry. Anal Biochem. 331, 27-32), and mass-tag labeled cross-linking reagents, for example as described in Tang, X., Munske, G. R., Siems, W. F., and Bruce, J. E. (2005) Mass Spectrometry Identifiable Cross-Linking Strategy for Studying Protein-Protein Interactions. Anal Chem 77, 311-318; and Back, J. W., Hartog, A. F., Dekker, H. L., Muijsers, A. O., de Koning, L. J., and de Jong, L. (2001) A New Crosslinker for Mass Spectrometric Analysis of the Quaternary Structure of Protein Complexes. J. Am. Soc. Mass Spectrom. 12, 222-227.

These methods can identify cross-linked peptides with MS analysis, but interpretation of the data generated from inter-linked peptides (two peptides connected with the cross-link) by automated database searching remains difficult. Several bioinformatics tools have thus been developed to interpret MS/MS data and determine inter-linked peptide sequences from complex mixtures, as described in Maiolica, A. et al.; Schilling, B. et al.; Chu, F., Baker, P. R., Burlingame, A. L., and Chalkley, R. J. (2009) Finding Chimeras: A Bioinformatic Strategy for Identification of Cross-Linked Peptides. Mol Cell Proteomics 9, 25-31; Gao, Q., Xue, S., Shaffer, S. A., Doneanu, C. E., Goodlett, D. R., and Nelson, S. D. (2008) Minimize the Detection of False Positives by the Software Program Detectshift for 18o-Labeled Cross-Linked Peptide Analysis. Eur J Mass Spectrom (Chichester, Eng) 14, 275-280; Singh, P., Shaffer, S. A., Scherl, A., Holman, C., Pfuetzner, R. A., Larson Freeman, T. J., Miller, S. I., Hernandez, P., Appel, R. D., and Goodlett, D. R. (2008) Characterization of Protein Cross-Links Via Mass Spectrometry and an Open-Modification Search Strategy. Anal Chem 80, 8799-8806; Rinner, O., Seebacher, J., Walzthoeni, T., Mueller, L. N., Beck, M., Schmidt, A., Mueller, M., and Aebersold, R. (2008) Identification of Cross-Linked Peptides from Large Sequence Databases. Nat Methods 5, 315-318; Lee, Y. J., Lackner, L. L., Nunnari, J. M., and Phinney, B. S. (2007) Shotgun Cross-Linking Analysis for Studying Quaternary and Tertiary Protein Structures. J Proteome Res 6, 3908-3917; and Nadeau, O. W., Wyckoff, G. J., Paschall, J. E., Artigues, A., Sage, J., Villar, M. T., and Carlson, G. M. (2008) Crosssearch, a User-Friendly Search Engine for Detecting Chemically Cross-Linked Peptides in Conjugated Proteins. Mol Cell Proteomics 7, 739-749.

Although promising, further developments are still needed to make such data analyses as robust and reliable as analyzing MS/MS data of single peptide sequences using existing database searching tools (e.g. Protein Prospector, Mascot or SEQUEST).

Various types of cleavable cross-linkers with distinct chemical properties have been developed to facilitate MS identification and characterization of cross-linked peptides. These include UV photocleavable (Nadeau, O. W., Wyckoff, G. J., Paschall, J. E., Artigues, A., Sage, J., Villar, M. T., and Carlson, G. M. (2008) Crosssearch, a User-Friendly Search Engine for Detecting Chemically Cross-Linked Peptides in Conjugated Proteins. Mol Cell Proteomics 7, 739-749), chemical cleavable (Kasper, P. T., et al.), isotopically-coded cleavable (Petrotchenko, E. V., et al.), and MS-cleavable reagents, as described in Tang, X, et. al.; Back, J. W., et. al.; Zhang, H., Tang, X., Munske, G. R., Tolic, N., Anderson, G. A., and Bruce, J. E. (2009) Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-Linking and Mass Spectrometry. Mol Cell Proteomics 8, 409-420; Soderblom, E. J., and Goshe, M. B. (2006) Collision-Induced Dissociative Chemical Cross-Linking Reagents and Methodology: Applications to Protein Structural Characterization Using Tandem Mass Spectrometry Analysis. Anal Chem 78, 8059-8068; Soderblom, E. J., Bobay, B. G., Cavanagh, J., and Goshe, M. B. (2007) Tandem Mass Spectrometry Acquisition Approaches to Enhance Identification of Protein-Protein Interactions Using Low-Energy Collision-Induced Dissociative Chemical Crosslinking Reagents. Rapid Commun Mass Spectrom 21, 3395-3408; Lu, Y., Tanasova, M., Borhan, B., and Reid, G. E. (2008) Ionic Reagent for Controlling the Gas-Phase Fragmentation Reactions of Cross-Linked Peptides. Anal Chem 80, 9279-9287; and Gardner, M. W., Vasicek, L. A., Shabbir, S., Anslyn, E. V., and Brodbelt, J. S. (2008) Chromogenic Cross-Linker for the Characterization of Protein Structure by Infrared Multiphoton Dissociation Mass Spectrometry. Anal Chem 80, 4807-4819.

MS-cleavable cross-linkers have received considerable attention since the resulting cross-linked products can be identified based on their characteristic fragmentation behavior observed during MS analysis. Gas-phase cleavage sites result in the detection of a “reporter” ion (Back, J. W., et al.), single peptide chain fragment ions (Soderblom, E. J., and Goshe; Soderblom, E. J., Bobay, B. G., et al.; Lu, Y., et al. and Gardner, M. W. et al.), or both reporter and fragment ions (Tang, X., et al.; and Zhang, H. et. al.).

In each case, further structural characterization of the peptide product ions generated during the cleavage reaction can be accomplished by subsequent MS^(n1) analysis. Among these linkers, the “fixed charge” sulfonium ion containing cross-linker developed by Lu. et. al appears to be the most attractive as it allows specific and selective fragmentation of cross-linked peptides regardless of their charge and amino acid composition based on their studies with model peptides.

Thus, in some embodiments, a novel cross-linking strategy for structural analysis of model proteins and the yeast 20 S proteasome complex by combining a newly designed MS-cleavable cross-linker bis(2,5-dioxopyrrolidin-1-yl) 3,3′-sulfinyldipropanoate (“DSSO”) with an integrated data analysis workflow is provided. As noted herein, while this discussion has centered around DSSO (shown as Compound 1 in FIG. 1), other compounds having the General Structure 2, such as Compounds 3-6 can also be used.

In some embodiments, an effective approach that facilitates fast and accurate identification of DSSO cross-linked peptides by LC MS^(n) is provided. In some embodiments, the new MS-cleavable cross-linker DSSO is attractive for cross-linking studies of protein complexes for a number of reasons: 1) it can be easily synthesized and can cross-link protein complexes effectively at sub-micromolar concentrations (˜1 μM); 2) it has two symmetric CID labile C—S bonds that preferentially fragment prior to peptide backbone breakage; 3) the CID-induced cleavage of inter-linked peptides is specific and independent of peptide charges and sequences; 4) DSSO cross-linked peptides can generate characteristic fragmentation patterns in MS/MS spectra that are unique to different types of cross-linked peptides for easy identification; 5) there are unique mass and charge relationships between MS/MS peptide fragment ions and their parent ions, permitting automated data processing.

In comparison to existing MS-cleavable cross-linkers (Tang, X., et al.; Zhang, H., et al.; Soderblom, E. J., and Goshe, M. B. et al.; Soderblom, E. J., Bobay, B. G., et al.; and Gardner, M. W., et al.), in some embodiments, the DSSO cross-linker can provide a specific and selective fragmentation of cross-linked peptides for identification. The fragmentation patterns of DSSO cross-linked peptides are similar to those of “fixed charge” sulfonium ion containing cross-linked model peptides developed by Lu, Y. et al.

Although DSSO does not carry a fixed charge, in some embodiments, the preferential cleavage of C—S bond adjacent to the sulfoxide in DSSO is as effective as cleavage of the C—S bond in the sulfonium ion containing cross-linker (i.e. S-methyl 5,5′-thiodipentanoylhydroxysuccinimide) (Lu, Y. et al.).

Fragmentation of the sulfonium ion containing cross-linked peptide requires the formation of a five-membered ring with the sulfonium ion and the amide of the linker such that it is not feasible to change spacer lengths in these cross-linkers. In contrast, in some embodiments, the simple fragmentation mechanism gives DSSO the flexibility of changing its spacer lengths to accommodate cross-linking lysines at different distances while maintaining the symmetry of the linker with easily interpretable fragmentation patterns.

In addition, in some embodiments, DSSO has better potential for studying protein interactions by in vivo cross-linking. It is well known that cross-linking study of protein complexes is extremely challenging due to the inherent limitations of current cross-linkers. With the improvement on database searching of non-cleavable inter-linked peptides, it is possible to identify cross-linked peptides of protein complexes using non-cleavable cross-linkers (Maiolica, A., et al.; and Chen, Z. A. et al.). However, this requires a special program for data interpretation and the false positive rate of identifying inter-linked sequences is higher than that of identifying single sequences.

Thus, in some embodiments, the feasibility of using novel DSSO cross-linking strategy to study the structure of the yeast 20S proteasome complex is provided, which is a significant advancement in structural elucidation of multi-subunit protein complexes with improved data analysis and accuracy as such application of MS-cleavable cross-linkers has not been reported before.

In addition to the design of this novel MS-cleavable linker, in some embodiments, an integrated data analysis workflow to achieve fast, easy and accurate identification of cross-linked peptides and the cross-linking sites is provided. Identification of DSSO cross-linked peptides from complex mixtures has been accomplished with high confidence by integrating data analyses of three different datasets, MS, MS/MS and MS³ data. Due to the difficulty in interpreting MS/MS spectra of unseparated inter-linked peptides, many of previously reported inter-linked products were determined only based on parent masses.

In contrast, in some embodiments, all of the inter-linked peptides of cytochrome c, ubiquitin and the yeast 20 S proteasome complex have been identified in this work with three lines of evidence including characteristic fragmentation pairs (Link-Finder), peptide sequence determination by MS³ sequencing (Batch-Tag), and mass mapping (MS-Bridge). In some embodiments, this procedure permits the identification of cross-linked peptides with high accuracy, reliability and speed. It is important to note that existing database search programs can be easily adapted for analyzing DSSO cross-linked peptides, thus a broad application of the DSSO-based cross-linking strategy is foreseeable. Furthermore, in some embodiments, cross-linked peptides of cytochrome c with two links can be identified, suggesting the capability of the new cross-linking strategy for identifying more complex cross-linked products.

Cross-linking/mass spectrometry has been previously attempted to study the yeast 20S proteasome complex using Ru(II)(bpy)^(2+/3) tris(2,2′-ipyridyl)ruthenium (II) dication)/ammonium persulfate /light-mediated cross-linking (Denison, C., and Kodadek, T. (2004) Toward a General Chemical Method for Rapidly Mapping Multi-Protein Complexes. J Proteome Res 3, 417-425), in which multiple subunit interconnectivity has been determined based on MS identification of co-migrated subunits by SDS-PAGE after cross-linking. No cross-linked peptides were identified due to complicated chemistry of the radical based cross-linking reaction.

Therefore, in some embodiments, a successful use of a cross-linking/mass spectrometry strategy to determine inter-subunit and intra-subunit interaction interfaces of the yeast 20 S proteasome complex. In some embodiments, although only 13 inter-linked peptides of the yeast 20 S proteasome have been identified and reported here, this disclosure presents the first step toward full characterization of proteasome structures using cross-linking/mass spectrometry in the future. The feasibility of using the DSSO-based cross-linking strategy to identify cross-linked peptides of a large protein complex at 1 μM or less concentration is very significant and of great promise to structural studies of protein complexes since purifying protein complexes at high concentrations is technically challenging.

During LC MS^(n) analysis using LTQ-Orbitrap XL MS, collision energy cannot be adjusted on the fly to account for differences in peptide charge states, therefore compromised collision energy is set during the entire LC MS^(n) run. Thus, it is contemplated that there exists a possibility that the collision energy may be too high for the highly charged ions while too low for peptides with lower charges. It is contemplated that future improvement on charge selection and energy adjustment during LC MS^(n) data acquisition may be needed to further enhance the quality of the results. Additionally, it is contemplated that optimized peptide separation prior to LC MS^(n) analysis will be necessary to improve the dynamic range of peptide analysis and allow the detection of low abundance cross-linked peptides. Moreover, it is contemplated that refinement of the Link-Finder program is needed to improve the identification of intra-linked peptides. Lastly, it is contemplated that the addition of an affinity tag to the sulfoxide containing cross-linker will improve detection of cross-linked peptides, which will be the subject of future study.

Thus, in some embodiments, a new MS-cleavable cross-linker family of compounds, including DSSO that are applicable for model peptides, proteins and a multi-subunit protein complex is provided. The unique MS features of DSSO cross-linked peptides together with the integrated data analysis workflow for analyzing LC MS^(n) data provided herein greatly reduce the time spent identifying cross-linked peptides. Given its simplicity, speed and accuracy, in some embodiments, this cross-linking strategy will have a broad application in elucidating structures of proteins and protein complexes in the future.

In some embodiments, a new crosslinking compound is provided and has the structure:

where x is selected from the group consisting of

wherein R is methyl or ethyl,

-   and

In some embodiments, the cross-linking agent is DSSO:

In some embodiments, the new cross-linking agents are used to facilitate mapping of protein-protein interactions of protein complexes. In some embodiments, the method comprises the steps of providing a MS-cleavable cross-linker having the structure described above; forming a cross-linked protein complex by cross-linking proteins with the MS-cleavable cross-linker; forming cross-linked peptide fragments that are chemically bound to the MS-cleavable cross-linker by digesting the cross-linked protein complex with an enzyme such as trypsin; and using mass spectrometry (MS) and MS^(n) analysis to identify the protein and/or peptide fragments. For convenience, in the discussion that follows, reference is sometimes made to the particular crosslinker, DSSO. It will be understood, however, that any of the other MS-cleavable crosslinkers that fit the general structure may also be used. Thus, DSSO fragments, DSSO remnants, DSSO cross-linked peptides, and like language applies equally to other crosslinkers as described herein.

The CID-induced separation of inter-linked peptides in MS/MS permits MS³ analysis of single peptide chain fragment ions with defined modifications (due to diamide remnants) for easy interpretation and unambiguous identification using existing database searching tools. Integration of data analyses from three generated datasets (MS, MS/MS and MS³) allows high confidence identification of DSSO cross-linked peptides. The efficacy of the newly developed DSSO-based cross-linking strategy has been demonstrated using model peptides and proteins. In addition, this method has been successfully employed for structural characterization of the yeast 20 S proteasome complex. In total, 13 non-redundant inter-linked peptides of the 20 S proteasome have been identified, representing the first application of an MS-cleavable cross-linker for the characterization of a multi-subunit protein complex. Given its effectiveness and simplicity, this cross-linking strategy can find a broad range of applications in elucidating structural topology of proteins and protein complexes.

In some embodiments, in combination with new software developed for data integration, DSSO cross-linked peptides were identified from complex peptide mixtures with speed and accuracy. Given its effectiveness and simplicity, in some embodiments, a broader application of this MS-cleavable cross-linker in the study of structural topology of other protein complexes using cross-linking and mass spectrometry is contemplated.

In order to develop a robust MS-cleavable cross-linking reagent, the incorporated MS-labile bond must have the ability to selectively and preferentially fragment prior to peptide backbone breakage independent of peptide charges and sequences. It is well documented that methionine sulfoxide containing peptides have preferential fragmentation at the C—S bond adjacent to the sulfoxide during collision induced dissociation (CID) analysis (see Reid, G. E., Roberts, K. D., Kapp, E. A., and Simpson, R. I. (2004) Statistical and Mechanistic Approaches to Understanding the Gas-Phase Fragmentation Behavior of Methionine Sulfoxide Containing Peptides. J Proteome Res 3, 751-759), and this fragmentation is dominant and much more labile than peptide bonds.

Such labile fragmentation has often been observed as the loss of 64 Da (—SOCH₄) from oxidized methionine containing peptides in routine peptide analysis. Therefore, in some embodiments, it is contemplated that if a sulfoxide is incorporated in the spacer region of a NHS ester, the C—S bond adjacent to the sulfoxide will be MS-labile and prone to preferential fragmentation.

In some embodiments, the synthesis of a CID cleavable cross-linker having a general structure of 3,3′-sulfinylbispropanoic acid, also known as 3,3-′sulfonyldipropanoic acid is provided. The molecular structure is C₆H₁₀O₅S, and it has a general structure as shown in General Structure 2 of FIG. 1 where X═—OH. In some embodiments, more specific cleaving agents are as shown in FIG. 1 including Compound 1, namely Disuccinimidyl Sulfoxide (sometimes hereinafter referred to as “DSSO”), which is one exemplary compound of the invention.

In some embodiments, other compounds where the X in the General Structure 2 are substituted are shown as Compounds 3-6 in FIG. 1. Hereinafter, while reference is made to DSSO, other MS-cleavable cross-linker having the general structure as shown in General Structure 2 of FIG. 1 are included as MS-cleavable cross-linkers of invention. Disuccinimidyl sulfoxide (DSSO) contains two NHS ester functional groups and two symmetric MS-labile C—S bonds adjacent to the sulfoxide (FIG. 2A). DSSO has a spacer length of 10.1 Å, making it well suited for detecting protein interaction interfaces of protein complexes and generating highly informative distance constraints. In comparison to existing MS-cleavable cross-linkers, DSSO can be easily synthesized in a two-step process as shown in FIG. 2A.

General chemicals were purchased from Fisher Scientific (Hampton, N.H.) or VWR International (West Chester, Pa.). Bovine heart cytochrome c (98% purity) and bovine erythrocyte ubiquitin (98% purity) were purchased from Sigma Aldrich (St. Louis, Mo.). Synthetic peptide Ac-IR7 (Ac-IEAEKGR (SEQ ID NO: 2), 98.1% purity) was synthesized by GL Biochem (Shanghai, China). Sequencing grade modified trypsin was purchased from Promega (Fitchburg, Wis.). The 20 S proteasome core particle was affinity purified using Prel-TAP expressing yeast strain as previously described in Leggett, D. S., Hanna, J., Borodovsky, A., Crosas, B., Schmidt, M., Baker, R. T., Walz, T., Ploegh, H., and Finley, D. (20032) Multiple Associated Proteins Regulate Proteasome Structure and Function. Mol Cell. 10, 495-507.

FIG. 2A displays a two-step synthesis scheme of DSSO with an extended spacer length of 10.1 Å. Sulfide S-1 was first synthesized by mixing 3,3′-thiodipropionic acid (2.50 g, 14.0 mmol) with N-hydroxysuccinimide (3.30 g, 28.6 mmol) in dioxane (60 ml). The reaction mixture was stirred under an atmosphere of argon, and a solution of DCC (5.79 g, 28.1 mmol) in dioxane (20 ml) was added drop-wise. After 12 h, the insoluble urea was filtered from the reaction. The filtrate was concentrated to form a white solid. The solid residue was washed with cold diethyl ether followed by cold hexanes. After drying under reduced pressure, 5.20 g (70%) of sulfide S-1 was recovered and used without further purification: 1H (500 MHz, DMSO-d6) δ 3.02 (t, J=7.0 Hz, 4H), 2.86 (t, J=7.0 Hz, 4H), 2.81 (s, 8H); ¹³C (125 MHz, DMSO-d6) δ 170.1, 167.8, 31.4, 25.6, 25.4; IR (KBr pellet) 1801, 1732 cm⁻¹; HRMS (ES/MeOH) m/z calcd for C₁₄H₁₆N₂O₈SNa [M+Na]⁺ 395.0525, found 395.0531.

In some embodiments, to synthesize DSSO, a solution of sulfide S-1 (0.600 g, 1.61 mmol) in CHCl₃ (30 ml) at 0° C. was mixed with a solution of m-chloroperbenzoic acid (MCPBA) (0.371 g, 1.61 mmol) in CHCl₃ (10 ml). The reaction product was filtered and washed with cold CHCl₃ (10 ml) and cold MeOH (10 ml). The filtrate was cooled to −10° C. for 1 h, washed again with CHCl₃ and MeOH, and dried under reduced pressure to yield 0.400 g (64%) of DSSO: 1H (600 MHz, DMSO-d6) δ 3.28-3.21 (m, 2H), 3.17-3.13 (m, 4H), 3.08-2.99 (m, 2H), 2.88-2.75 (s, 8H); ¹³C (125 MHz, DMSO-d6) δ 170.08, 167.74, 44.62, 25.46, 23.41; IR (KBr pellet) 2943, 1786, 1720 cm⁻¹; HRMS (ES/MeOH) m/z calculated for C₁₄H₁₆N₂O₉Na [M+Na]⁺ 411.0474, found 411.0471.

In some embodiments, a similar synthetic approach is used to make the other symmetric diesters identified above and having the general structure 2, where X is as defined above. Thus, the symmetric sulfide is prepared by reacting 3,3′-thiodipropionic acid with the appropriate N-hydroxyamine (e.g., a functionalized analogue of N-hydroxysucinimide (compounds 4-7), or other N-hydroxy-functionalized heterocycle (compounds 3, 8, and 9), and then the sulfinyl group is made by treating the symmetric sulfide with MCPBA in CHCl₃ or another appropriate solvent.

CID Fragmentation Pattern of DSSO Cross-Linked Peptides

Three types of cross-linked peptides can be formed during the cross-linking reaction: inter-linked (type 2), intra-linked (type 1) and dead-end (type 0) modified peptides (Schilling, B., et al.), among which inter-linked peptides are the most informative for generating distance constraints. FIGS. 2B-D shows the proposed fragmentation schemes of DSSO cross-linked peptides. As shown in FIG. 2B, during CID analysis of a DSSO inter-linked peptide α-β, the cleavage of one C—S bond next to the sulfoxide separates the inter-linked peptide into a pair of peptide fragments, i.e. α_(A)/β_(S), in which the a peptide fragment is modified with the alkene (A) moiety (+54 Da) and the β peptide fragment is modified with the sulfenic acid (S) moiety (+104 Da).

If peptides α and β have different sequences, two possible pairs of fragments (i.e. α_(A)/β_(S) and α_(S)/β_(A)) will be observed due to the breakage of either of the two symmetric C—S bonds next to the sulfoxide in the spacer region of DSSO (FIG. 2B), thus resulting in four individual peaks in the MS/MS spectrum. But if peptides α and β have the same sequences, only one fragment pair, i.e. two peaks, will be detected in the MS/MS spectrum. To determine sequences of inter-linked peptides and assign the cross-linking site, the resulting peptide fragments (i.e. α_(A), β_(S), α_(S), or β_(A)) generated in MS/MS can be further subjected to LTQ-Orbitrap XL MS for MS³ analysis. Because these fragments represent single peptide sequences, the interpretation of the MS³ spectra by Batch-Tag program in Protein Prospector is identical to the identification of a single peptide with a defined modification (remnant of the cross-linker). This will dramatically simplify data interpretation and improve the identification accuracy of cross-linked products.

DSSO dead-end modified peptides have a defined mass modification (+176 Da) due to the half-hydrolyzed DSSO (FIG. 2C). MS/MS analysis of a dead-end modified peptide α_(DN) would result in two possible fragment ions, i.e. α_(A) and α_(S), due to the cleavage of the C—S bond on either side of the sulfoxide. The α_(A) and α_(S) fragments are called dead end fragment pair and the mass difference between these fragments correlates to the difference between the remnants of DSSO attached to the fragments. Similarly, intra-linked peptides (e.g. α_(intra)) also have a defined mass modification (+158 Da) due to DSSO cross-linking of two distinct lysines in the same peptide sequence (FIG. 2D). The cleavage of the C—S bond will result in only one fragment peak in MS/MS with the same mass as the parent ion observed in MS. MS³ analysis of fragment ions detected in MS/MS will lead to the detection of y or b ions containing either alkene (A) or sulfenic acid (S) modifications.

As shown in FIG. 2E, the sulfenic acid containing fragment (e.g. α_(S), β_(S), or α_(A+S)) may undergo further fragmentation and lose a water molecule (−18 Da) to generate a new fragment containing an unsaturated thiol (T) moiety (+86 Da) (e.g. α_(T), β_(T), or α_(A+T)). Complications with data analysis are not expected as the thiol-containing fragment ion will become the dominant ion instead of the sulfenic acid modified fragment ion in the MS/MS spectrum. Thus, it is contemplated that the total number of pairs and peaks will remain similar as shown in FIGS. 2B-D. Due to specific and unique MS/MS fragmentation patterns for different types of DSSO cross-linked peptides, there are fixed mass relationships between parent ions and their fragment ions as listed in FIG. 2F.

For DSSO inter-linked peptides (α-β), the mass sum of each fragment pair (α_(A)/β_(S) or α_(S)/β_(A)) is equivalent to the mass of the parent ion (FIG. 2F, Eq. 1). If α_(S) or β_(S) loses a water and becomes α_(T) or β_(T) respectively, the fragment pairs will be α_(A)/β_(T) and α_(T)/β_(A) and the mass sum of each fragment pair plus a water will be the same as the parent mass (FIG. 2F, Eq. 2).

As for the dead-end (DN) modified peptide α_(DN), each fragment (i.e. α_(A), α_(S) or α_(T)) has a distinct mass difference from the parent ion (FIG. 2F, Eq. 3). For the intra-link peptide aintra, the fragment mass could be either the same as the parent mass (i.e. α_(A+S)), or 18 Da less than the parent mass (i.e. α_(A+T)) (FIG. 2F, Eq. 4). Moreover, there is a definite mass difference (Δ 32 Da) between the thiol (T) and alkene (A) modified forms of the same sequence (FIG. 2F, Eq. 5). These characteristic mass relationships have been incorporated into the Link-Finder program to identify DSSO cross-linked peptides.

LC MS^(n) analysis of DSSO cross-linked peptides was performed using a LTQ-Orbitrap XL MS (Thermo Scientific, San Jose, Calif.) with an on-line Eksigent NanoLC system (Eksigent, Dublin, Calif.). The LC separation was the same as previously described by Vellucci, D., et al. The MS^(n) method was set specifically for analyzing DSSO cross-linked peptides. Each acquisition cycle of a MS^(n) experiment includes one MS scan in FT mode (350-1800 m/z, resolution of 60,000 at m/z 400) followed by two data-dependent MS/MS scans with normalized collision energy at 10 or 15% on the top two peaks from the MS scan, and then three MS³ scans operated in LTQ with normalized collision energy at 29% on the top three peaks from each of the MS/MS scans. For initial analyses, MS/MS spectra were acquired in LTQ in LC MS^(n) experiments. For automated data analysis, MS/MS spectra were obtained in FT mode (resolution of 7500).

Characterization of DSSO Cross-Linked Model Peptides by MS^(n) Analysis

In some embodiments, in order to characterize the new DSSO linker, several model peptides were cross-linked including Ac-IR7, Ac-myelin, and substance P. Under the experimental conditions, the major cross-linked products for Ac-IR7 and Ac-myelin are inter-linked, whereas substance P mostly formed dead-end modified peptides. All of the cross-linked model peptides were subjected to LC MS^(n) analysis. The inter-linked Ac-IR7 peptide (α-α) was detected as doubly charged (m/z 923.46²⁺) and triply charged (m/z 615.97³⁺) ions (FIG. 3A). MS/MS analyses of the two differently charged parent ions resulted in two dominant fragment ions respectively (FIGS. 3B-C).

Cross-linking of synthetic peptides with DSSO was performed by dissolving synthetic peptides Ac-IR7, Ac-myelin and substance P in DMSO to 1 mM and cross-linked with DSSO dissolved in DMSO in a ratio of 1:1 in the presence of 1 equivalent diisopropylethylamine similarly as described Vellucci, D, et al. The cross-linked peptide solution was then diluted to 1 pmol/μl in 4% ACN, 0.1% formic acid for liquid chromatography multi-stage tandem mass spectrometry (LC MS^(n)) analysis.

Since the two inter-linked sequences are identical, only one fragment pair (i.e. α_(A)/α_(S)) was observed as expected. The results suggest that MS/MS fragmentation of inter-linked peptides is independent of peptide charges. It should be noted that besides unique mass relationships, the fragment ions in each pair have a defined charge relationship associated to the charge of the parent ion. In other words, the sum of the observed charges for each fragment in a pair equals the charge of the parent ion. For example, the triply charged parent ion (m/z 615.97³⁺) generated the fragment pair with one doubly charged (α_(A) ²⁺) and one singly charged (α_(S) ¹⁺) ion, whereas the doubly charge parent ion (m/z 923.46²⁺) only produced a fragment pair with two singly charged (α_(A) ¹⁺ and α_(S) ¹⁺) ions.

This information can be used to validate the fragment pairs identified by masses. The respective MS³ analysis of α_(A) and α_(S) ions (FIGS. 3D-E) allowed unambiguous identification of the peptide sequence and cross-linked site based on a series of y and b ions. Similar analysis was carried out for inter-linked Ac-myelin (β-β), and a characteristic fragment pair was observed in MS/MS spectra of the parent ion (β-β at three different charge states (m/z 458.23⁶⁺, 549.68⁵⁺, 686.84⁴⁺) respectively (FIGS. 3F-I), which represent the expected fragmentation of two identical inter-linked peptides.

While the fragment pair β_(A)/β_(S) was detected in MS/MS spectra of quintuply and quadruply charged inter-linked Ac-myelin (β-β) (m/z 549.68⁵⁺, 686.84⁴⁺) (FIGS. 2H-I), the fragment pair β_(A)/β_(T) was observed in the MS/MS spectrum of sextuply charged inter-linked Ac-myelin (β-β) (458.23⁶⁺) (FIG. 3G). The β_(T) fragment, namely the β peptide fragment containing an unsaturated thiol (T) moiety (+86 Da), was generated due to the loss of H₂O from the sulfenic acid moiety on the β_(S) fragment (FIG. 2E). This is likely due to excess collision energy deposited on the highest charged species as the collision energy chosen for CID analysis in LTQ-Orbitrap XL MS does not change with peptide charges during LC MS^(n) runs.

In addition to inter-linked peptides, dead-end modified peptides were analyzed. FIG. 2J displays the MS spectrum of the dead-end (DN) modified substance P (γ_(DN), m/z 538.76²⁺). As predicted in FIG. 2D, MS/MS analysis of γ_(DN) led to two major fragments, the alkene (γA, m/z 478.03²⁺) and sulfenic acid (γ_(S), m/z 502.95²⁺) containing peptide fragments, representing the characteristic feature of dead-end modified peptides. The fragment ions carry the same charge state as the parent ion, and MS³ analysis of the γ_(A) fragment confirmed its sequence unambiguously (FIG. 3L). Taken together, the results clearly demonstrate that the new MS-cleavable bonds in DSSO are labile and can be preferentially fragmented prior to peptide bond breakage, and the desired fragmentation is independent of peptide charge states and sequences.

Characterization of DSSO Cross-Linked Peptides of Model Proteins by MS^(n) Analysis

In some embodiments, the applicability of DSSO for protein cross-linking under physiological conditions was evaluated. Model proteins cytochrome c (see for previously described Sinz, A. (2003); Kasper, P. T., et al.; Nessen, M. A., et al.; Vellucci, D., et al.; Lee, Y. J., et al.; Pearson, K. M., Pannell, L. K., and Fales, H. M. (2002) Intramolecular Cross-Linking Experiments on Cytochrome C and Ribonuclease a Using an Isotope Multiplet Method. Rapid Commun. Mass Spectrom. 16, 149-159; Dihazi, G. H., and Sinz, A. (2003) Mapping Low-Resolution Three-Dimensional Protein Structures Using Chemical Cross-Linking and Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry. 17, 2005-2014; and Guo, X., Bandyopadhyay, P., Schilling, B., Young, M. M., Fujii, N., Aynechi, T., Guy, R. K., Kuntz, I. D., and Gibson, B. W. (2008) Partial Acetylation of Lysine Residues Improves Intraprotein Cross-Linking. Anal Chem 80, 951-960) and ubiquitin (Chowdhury, S. M., et al.; and Gardner, M. W., et al.) have been extensively utilized to test various new cross-linking strategies since they have a relatively large number of lysine residues accessible for cross-linking.

Cross-linking of Cytochrome C and Ubiquitin with DSSO was performed using lyophilized bovine cytochrome c or ubiquitin reconstituted in 1× PBS (pH 7.5) to 200 μM, 20 μl of which was mixed with 2 μl 20 mM DSSO (in DMSO) in a molar ratio of 1:10 (protein:cross-linker) for the cross-linking reaction as described in Vellucci, D., et al. The cross-linked protein was digested with trypsin (1% w/w) overnight at 37° C. The cross-linked peptide digest was then diluted to 1 pmol/μl in 4% ACN, 0.1% formic acid for LC MS^(n) analysis.

Based on previous work (see Vellucci, D., et al.), cytochrome c was cross-linked with a 10-fold excess of DSSO. The cytochrome c cross-linking efficiency using DSSO was comparable to the efficiency using DSG or previously developed Azide-DSG cross-linkers (see Vellucci, D., et al.), indicating that DSSO is as effective for protein cross-linking reactions. The DSSO cross-linked cytochrome c was then digested with trypsin and analyzed by LC MS^(n). Three types of cross-linked peptides of cytochrome c (i.e. inter-link, intra-link and dead-end) have been observed. FIG. 4A displays the MS/MS spectrum of a tryptic peptide of cytochrome c with m/z 419.9716⁴⁺, in which only four abundant fragment ions (m/z 336.42²⁺, 352.40²⁺, 478.99²⁺, 494.96²⁺) were detected, suggesting this peptide as a potential heterodimeric inter-linked peptide (α-β).

Two possible fragment pairs, α_(A)/β_(S)/_(T) and α_(S/T)/β_(A) are thus expected, in which S/T means either S (sulfenic) or T (unsaturated thiol) containing fragment ions will be observed. Using the mass relationship between the pairs and the parent ion of inter-linked peptides (Eqs. 1, 2, 5 in FIG. 2F), two fragment pairs as α_(A)/β_(T) (478.99²⁺/352.40²⁺) and α_(T)/β_(A) (494.96²⁺/336.42²⁺) were identified, confirming that this peptide is a heterodimeric inter-linked peptide (α-β).

Mass mapping of the parent ion (m/z 419.9716⁴⁺) by MS-Bridge revealed that it matches to an inter-linked peptide [Ac-GDVEKGKK (SEQ ID NO: 11) inter-linked to KKGER (SEQ ID NO: 13)] with an error of 0.48 ppm. The fragment ions α_(A) (m/z 478.99²⁺) and β_(T) (m/z 352.40²⁺) were further subjected to MS³ sequencing and their MS³ spectra are illustrated in FIGS. 4B-C. Based on the series of y (i.e. y₁₋₇) and b (i.e. b₂₋₇) ions, the sequence of the MS/MS fragment ion α_(A) (m/z 478.99²⁺) was unambiguously identified as Ac-GDVEK_(A)GKK (SEQ ID NO: 12), in which K (Lys) at 5th position from N-terminus was determined to be modified with the alkene moiety. MS³ analysis of the corresponding fragment pair ion β_(T) (m/z 352.40²⁺) determined its sequence as K_(T)KGER (SEQ ID NO: 14). Although there are two lysine residues in the sequence, occurrence of y₄ and y₁ ions indicates that the first N-terminal K is modified with an unsaturated thiol moiety. Taken together, the identity and cross-linking site of the inter-link peptide [Ac-GDVEKGKK (SEQ ID NO: 11) inter-linked to KKGER (SEQ ID NO: 13)] was determined unambiguously.

FIGS. 5A-C display MS/MS spectra of triply (m/z 641.6730³⁺), quadruply (m/z 481.5069⁴⁺), and quintuply (m/z 385.4070⁵⁺) charged ions of a cytochrome c cross-linked peptide. The MS/MS spectrum of the triply charged ion (m/z 641.6730³⁺) resulted in four dominant fragment ions (m/z 386.24, 418.21, 744.40²⁺, 760.38²⁺), which have been determined as the two fragment pairs α_(A)/β_(T) (744.40²⁺/418.21) and α₁/β_(A) (760.38²⁺/386.24), indicating this peptide is a heterodimeric inter-linked peptide. The same characteristic fragment pairs, i.e. α_(A)/β_(T) and α₁/β_(A) have also been identified but with different charges in the MS/MS spectra of the quadruply (m/z 481.5069⁴⁺) and quintuply (m/z 385.4070⁵⁺) charged parent ions respectively (FIGS. 5B-C).

It is noted that some charge distribution of fragment ions was observed in the pairs (FIG. 5C) due to the high charge state of the parent ion. Nevertheless, the dominant ions are the characteristic fragment ions of the inter-linked peptide. MS³ analysis of the α_(A) (m/z 496.60³⁺) fragment has revealed its sequence identity unambiguously as HK_(A)TGPNLHGLFGR (SEQ ID NO: 17), in which the K (Lys) at position 2 from N-terminus was modified with the alkene moiety (FIG. 5D). In combination with the MS-Bridge result, the inter-linked peptide is identified as [HKTGPNLHGLFGR (SEQ ID NO: 16) inter-linked to GKK]. These results demonstrate that preferred fragmentation of the C—S bonds in DSSO inter-linked peptides of cytochrome c occurs as expected and is independent of peptide charge states and sequences.

To understand how dead-end modified peptides of cytochrome c behave in MS^(n) analysis, FIG. 6A illustrates the MS/MS spectrum of a selected dead-end modified peptide (m/z 880.8975²⁺). As shown, two major fragment ions (m/z 820.20²⁺ and 835.88²⁺) were detected and they are 122 and 90 Da less than the parent ion respectively. Such mass differences between the parent ion and its fragment ions fit well with those predicted for DSSO dead-end modified peptides (eq. 3 in FIG. 2F), identifying the ion m/z 820.20²⁺ as α_(A) and 835.88²⁺ as α_(T) fragment. MS³ analysis of the α_(A) fragment (m/z 820.20²⁺) (FIG. 6B) as well as the MS-Bridge result of the parent ion (m/z 880.8975²⁺) identified its sequence as K_(DN)TGQAPGFSYTDANK (SEQ ID NO: 20).

As discussed above (FIG. 2D), in some embodiments, it is contemplated that MS/MS analysis of the intra-linked peptide (α_(mtra)) will lead to either a fragment ion (α_(A+S)) containing one K_(A) (Lys_(A)) and one K_(S) (Lys_(S)) with the same mass as the parent ion or a fragment ion (α_(A+T)) containing one K_(A) (Lys_(A)) and one K_(S) (Lys_(T)) with a mass 18 Da less than the original parent ion. FIG. 6C displays the MS/MS spectrum of a cytochrome c tryptic peptide with m/z 611.9802³⁺ in which only one major fragment ion (m/z 606.24²⁺) was detected with a mass 18 Da less than the parent ion.

This suggests that the peptide is potentially an intra-linked peptide of cytochrome c and its MS/MS fragment ion (m/z 606.24²⁺) can be labeled as α_(A+T). Mass mapping of the parent ion m/z 611.9802³⁺ using MS-Bridge matched to an intra-linked peptide, GGK*HK*TGPNLHGLFGR (SEQ ID NO: 24), where the two N-terminal K* (Lys*) are linked. Since the CID-induced C—S bond breakage can occur at either side of the sulfoxide, a mixture of two fragments with identical masses but with alkene (A) or thiol (T) moieties at either K can be generated.

FIG. 6D illustrates the MS³ spectrum of the MS/MS fragment ion (m/z 606.24³⁺), with a series of y and b ions confirming its identity as GGK_(T)HK_(A)TGPNLHGLFGR (SEQ ID NO: 26) and/or GGK_(A)HK_(T)TGPNLHGLFGR (SEQ ID NO: 25). The detection of y₁₃ (760.43²⁺), and b₃ (297.34) ions indicates the presence of the peptide fragments from the sequence of GGK_(T)HK_(A)TGPNLHGLFGR (SEQ ID NO: 26), and the detection of b₃* (329.37), b₄* (466.33), γ₁₂* (692.10²⁺), and γ₁₃*(744.51²⁺) identified the peptide fragments from the GGK_(A)HK_(T)TGPNLHGLFGR (SEQ ID NO: 25) sequence.

Development of an Integrated Workflow for Fast and Accurate Identification of DSSO Cross-Linked Peptides by LC MS^(n)

In order to facilitate data analysis for the identification of DSSO cross-linked peptides from complex mixtures, an integrated workflow for processing LC MS^(n) data acquired by LTQ-Orbitrap XL MS was developed (FIG. 7A). During LC MS^(n) analysis, three types of data are collected, i.e. MS, MS/MS and MS³ spectra, in which MS and MS/MS are acquired in FT mode to allow accurate mass measurement and charge determination of both parent ions in MS and their fragment ions in MS/MS spectra. MS³ is obtained in LTQ to achieve the highest sensitivity. As shown, the first data extraction step is to generate the text files containing peak lists of MS/MS and MS³ data respectively.

Based on the unique MS/MS fragmentation profiles of DSSO cross-linked peptides and the defined mass relationships between parent ions and their fragment ions (FIG. 2), Link-Finder program was developed to automatically search MS/MS data to identify putative DSSO cross-linked peptides (FIG. 7B). As discussed above, the inter-linked products produce distinct MS/MS spectra with two pairs of dominant peptide fragments (α_(A)/β_(S/T) and α_(T/S)/β_(A)). For each MS/MS scan, among the top eight most abundant peaks, if there is a fragment pair with a mass sum equal to their parent mass with or without a water loss (−18 Da), the parent ion will be categorized as a possible inter-linked peptide.

If two of those pairs can be found, and the mass difference between any two fragments from the two distinct pairs is 32 Da, i.e., the mass difference between the thiol and alkene moieties, then it is almost certain that the parent ion is a true inter-linked product. The dead-end product typically has two major fragment ions representing the parent peptide attached with either a thiol or an alkene moiety. Among the top three peaks, if there are two peaks with mass difference of 32 Da, and one of them is 90 Da less than the parent mass, then it is categorized as a possible dead-end peptide. Using the Link-Finder program, a list of parent ions are identified as putative inter-linked or dead-end modified peptides. The generated list of parent ion masses is then subjected to MS-Bridge to identify putative cross-linked peptides of all types by mass matching with high mass accuracy (<10 ppm).

For MS³ data, only the original parent ion observed in MS scan is listed as the precursor ion during database searching. In order to extract the MS³ parent ion (fragment ions in MS/MS), for Batch-Tag search, the second data extraction step is carried out using in-house scripts to generate a modified MS³-txt file. The Batch-Tag search result provides high confidence identification of single peptide fragments generated in MS/MS that are initially cross-linked. Finally, the results from three different types of searches, i.e. Batch-Tag (MS³ data), Link-Finder (MS/MS data), and MS-Bridge (MS data) are integrated using in-house scripts within Link-Finder program to obtain accurate and reliable identification of cross-linked peptides. Among them, MS³ sequencing with Batch-Tag searching is essential for unambiguous identification of cross-linking sites.

Identification of DSSO Cross-Linked Peptides of Model Proteins by Automated Database Searching

The newly developed integrated workflow was first employed to identify DSSO cross-linked peptides of cytochrome c. In total, 19 inter-linked peptides have been unambiguously identified and summarized in TABLE 1 (for details see TABLE 3). Each peptide has characteristic fragment pairs in MS/MS spectra and was identified by Link-Finder program. In addition, one or two MS/MS fragment pair ions have been sequenced by MS³ to provide unambiguous identification. Moreover, all of the parent masses fit well with identified cross-linked peptides by MS-Bridge program with high mass accuracy. In comparison to reported cross-linking studies of cytochrome c (Schilling, B., et al.; Kasper, P. T. et al.;Nessen, M. A. et al.; Vellucci, D. et al.; Lee, Y. J., et al.; Pearson, K. M., et al.; Dihazi, G. H.; and Guo, X., et al.), three novel inter-links have been identified in this work. Besides the inter-linked peptides, 7 intra-linked and 8 dead-end peptides have also been identified (See TABLE 3). For the dead-end modified peptides, each has a dead-end fragment pair and at least one of the fragment ions has been sequenced, which correlates very well with MS-Bridge and Batch-Tag results. The intra-linked peptides were mainly identified by Batch-Tag and MS-Bridge results.

In addition to products with one cross-link (i.e. type 0, 1 and 2), peptides containing two cross-links have also been identified using this integrated workflow. In this work, 11 non-redundant DSSO cross-linked peptides with two links (e.g. one inter-link with one dead-end, one inter-link with one intra-link, or one intra-link with one dead-end) have been identified and summarized in TABLE 3. This type of information is not commonly reported since peptide sequencing of multi-linked peptides is highly complicated. This demonstrates the ability of the new cross-linking strategy provided herein for identifying such complex products.

Based on the crystal structure of bovine heart cytochrome c (PDB ID; 2B4Z) (44), the distances between alpha carbons of the identified cross-linked lysine residues were calculated (TABLE 1 and TABLE 3). Among the 26 non-redundant inter-linked lysines in cytochrome c identified in this work (excluding linkages between two adjacent lysines), all of the linkages have the distances between their alpha carbons within the range of 5.3 Å to 19.3 Å. This is consistent not only with the length of a fully expanded DSSO (10.1 Å spacer length) and two lysine side chains, but also with the previous results using similar lengths of NHS ester cross-linkers (see Vellucci, D., et al.; Lee, Y. J., et al.; Guo, X., et al.; and Kruppa, G. H., Schoeniger, J., and Young, M. M. (2003) A Top Down Approach to Protein Structural Studies Using Chemical Cross-Linking and Fourier Transform Mass Spectrometry. Rapid Commun Mass Spectrom 17, 155-162). The results suggest that the cross-linking conditions herein did not induce significant disturbance to cytochrome c structural conformations.

In addition to cytochrome c, the same strategy has been successfully applied to identify DSSO cross-linked peptides of ubiquitin. Using the same analysis strategy, 3 inter-linked, 1 intra-linked, and 5 dead-end peptides have been identified as summarized in TABLE 4. Based on the crystal structure of bovine ubiquitin (PDB ID; 1AAR), all of the identified inter-/intra-linked lysines in ubiquitin have the distances between their alpha carbons within the range of 6 to 18 Å. The identified cross-linked lysines are consistent with the known structure of ubiquitin and previous reports (Chowdhury, S. M., et al.; and Gardner, M. W., et al.)

It is interesting to note that one of the identified inter-linked peptides is [LIFAGK⁴⁸QLEDGR (SEQ ID NO: 63) inter-linked to LIFAGK⁴⁸QLEDGR (SEQ ID NO: 63)], which is a cross-link formed between the ubiquitin dimer. Residue K⁴⁸ is located at a hydrophobic patch important for protein interactions and K⁴⁸ is also an in vivo chain linkage site for polyubiquitination required for ubiquitin/ATP dependent proteasomal degradation (Pickart, C. M., and Cohen, R. E. (2004) Proteasomes and Their Kin: Proteases in the Machine Age. Nat Rev Mol Cell Biol. 5, 177-187). The same K48-K48(Lys⁴⁸-Lys⁴⁸) cross-link was identified previously using an alkyne-tagged NHS ester, but only after selective enrichment coupled with CID and ETD analyses (Chowdhury, S. M., et al.). In comparison, in some embodiment, the K⁴⁸ inter-linked peptide without any enrichment was identified, thus further demonstrating the effectiveness of the approach disclosed herein to identify DSSO cross-linked peptides from complex mixtures.

Structural Elucidation of the Yeast 20 S Proteasome Complex Using DSSO Cross-Linking

The ubiquitin-proteasome degradation pathway plays an important role in regulating many biological processes (Pickart, C. M., et al.) The 26 S proteasome complex is the macromolecular machine responsible for ubiquitin/ATP dependent protein degradation, and it is composed of two subcomplexes: the 20S core particle and the 19 S regulatory complex. To date, only the crystal structure of the 20 S proteasome complex has been resolved. However, structures of the 19 S and 26 S remain elusive, thus hindering the understanding of the structure and functional relationship of the 26 S proteasome complex. To develop an effective cross-linking strategy to elucidate structures of the 19 S and 26 S proteasome complexes, the structure of the yeast 20 S proteasome complex using the DSSO cross-linking approach was investigated.

In some embodiments, cross-linking of the Yeast 20 S Proteasome with DSSO was performed. Affinity purified yeast 20S proteasome complex was concentrated by Microcon (Billerica, Mass.) to ˜1.2 μM in 1× PBS buffer (pH 7.5). Typically 50 μl of the 20S proteasome was cross-linked with 3 μl DSSO (20 mM) dissolved in DMSO (final concentration ˜1 mM) at a molar ratio of 1:1000 (protein:cross-linker). Cross-linking was performed for a half hour or overnight and quenched with excess ammonium bicarbonate buffer. Cysteine residues were reduced with 5 mM DTT at 56° C. for 30 mins, and alkylated with 10 mM choloroacetamide for 30 min at room temperature. The cross-linked protein complex was digested with trypsin (2% w/w) overnight at 37° C. Digested peptides were desalted by C18 OMIX ZipTip (Varian, Palo Alto, Calif.) prior to LC MS^(n) analysis.

For some analyses, 2-dimensional LC MS^(n) analysis was carried out. Off-line strong cation exchange (SCX) chromatography was performed as the first dimension of separation using an AKTA HPLC system (GE Healthcare Life Sciences, Uppsala, Sweden) as described in Kaake, R. M., et al. Each fraction was desalted by ZipTip prior to LC MS^(n) analysis.

The cross-linking of the 20 S proteasome complex was carried out in PBS buffer under conditions allowing efficient cross-linking of all subunits as based on 1-D SDS-PAGE (FIG. 11). The tryptic digest of the cross-linked proteasome complex was subjected to LC MS^(n) analysis and the data were analyzed using the integrated work flow described above (FIG. 7). In total, 13 unique inter-linked peptides were identified including 10 intra-subunit and 3 inter-subunit heterodimeric inter-links as summarized in TABLE 2 (for details see TABLE 5), which were determined unambiguously by integration of Link-Finder, Batch-Tag (MS³ sequencing), and MS-Bridge (mass mapping of the cross-linked peptides) results.

As an example, FIG. 8A displays the MS/MS spectrum of a DSSO heterodimeric inter-linked peptide α-β (m/z 833.9231⁴⁺) of the yeast 20 S proteasome complex, in which two fragment pairs were detected and determined as α_(A)/β_(T) (868.45²⁺/790.39²⁺) and α_(T)/β_(T) (884.44²⁺/774.41²⁺). MS³ analysis of the α_(A) fragment (m/z 868.45²⁺) identified the a chain unambiguously as NK_(A)PELYQIDYLGTK (SEQ ID NO: 28), which matched to 20 S subunit β4. In this sequence, K_(A) is modified with the alkene moiety. In addition, MS³ analysis of the β_(T) fragment (m/z 790.39²⁺) identified the β chain unambiguously as LGSQSLGVSNK_(T)FEK (SEQ ID NO: 30), which matched to 20 S subunit β3. Here, K_(T) is modified with an unsaturated thiol moiety. Mass mapping by MS-Bridge further confirmed this inter-subunit (β4-β3) inter-linked peptide as [NKPELYQIDYLGTK (SEQ ID NO: 27) inter-linked to LGSQSLGVSNKFEK (SEQ ID NO: 29)].

In addition, 21 dead-end modified peptides were identified by multiple lines of evidence as illustrated in TABLE 5. The fragmentation behavior for the dead-end modified peptides of the 20 S subunits is the same as that of cytochrome c showing two distinct dead-end pairs in MS/MS spectra. This is illustrated with an example shown in FIG. 12.

The experimentally determined structure of the yeast 20 S proteasome holocomplex was utilized (Protein Data Bank code 1RYP) to assess the cross-linked lysine pairs identified in this study. For each identified cross-link the distance between the alpha carbons was calculated and the results are summarized in TABLE 2. Considering the spacer length of DSSO and lysine side chains, the theoretical upper limit for the distance between the alpha carbon atoms of paired lysines is approximately 26 Å. In some embodiments, the distances are within this upper limit, providing some evidence that the proteasome cross-links are formed in the native state. The quaternary proteasome structure is formed by four stacked seven-member rings in the order αββα. The side view and basal view of the arrangement among one set of the symmetric αβ rings and their subunits are shown in FIG. 9. The alpha carbon trace is shown for all subunits and the cross-linked lysines are shown in space fill representation. Lysines forming intra-subunit cross-links appear in blue and those forming inter-subunit cross-links appear in red. The images in FIG. 9 were generated using UCSF Chimera visualization software (Pettersen, E., Goddard, T., Huang, C., Couch, G., Greenblatt, D., Meng, E., and Ferrin, T. (2004) Ucsf Chimera—a Visualization System for Exploratory Research and Analysis. Journal of computational chemistry 25, 1605-1612).

Data Analysis of DSSO Cross-linked Peptides as follows. Monoisotopic masses of parent ions and corresponding fragment ions, parent ion charge states and ion intensities from LC MS/MS and LC MS³ spectra were extracted using in-house software based on Raw_Extract script from Xcalibur v2.4 (Thermo Scientific, San Jose, Calif.). Database searching was performed with a developmental version of Protein Prospector (v. 5.5.0, University of California, San Francisco) (http://prospector.ucsf.edu/prospector/mshome.htm) using its software suite, i.e. Batch-Tag and MS-Bridge as described in Chu, F., et al. Using in-house scripts, extracted MS³ data were reformatted such that MS³ fragment ions were directly linked to their MS/MS parent ions.

For cytochrome c (P62894) and ubiquitin (P62990) analyses, database searching of MS³ spectra was performed using Batch-Tag against their accession numbers in SwissProt.2009.09.01 database. For the 20S proteasome, Batch-Tag search of MS³ data was performed against a decoy database consisting of a normal SGD yeast database concatenated with its reversed version (total 13490 protein entries). The mass tolerances for parent ions and fragment ions were set as ±20 ppm and 0.6 Da, respectively. Trypsin was set as the enzyme and a maximum of two missed cleavages were allowed. Protein N-terminal acetylation, methionine oxidation, and N-terminal conversion of glutamine to pyroglutamic acid were selected as variable modifications. In addition, three defined modifications on uncleaved lysines were chosen, including alkene (C₃H₂O, +54 Da), sulfenic acid (C₃H₄O₂S, +104 Da), and thiol (C₃H₂SO, +86 Da) modifications due to remnants of the cross-linker (FIG. 1). Initial acceptance criteria for peptide identification required a reported expectation value ≦0.05. For the 20S proteasome analysis, the false positive rate for peptide identification is less than 1%.

The Link-Finder program (http://www.ics.uci.edu/˜baldig/Link-Finder/) was developed to search MS/MS data and identify the list of putative DSSO inter-linked and dead-end products based on their unique MS fragmentation patterns as illustrated in FIG. 2 (details see results section). For example, one embodiment of the invention includes identifying the MS/MS data that display characteristic fragmentation profiles of DSSO cross-linked peptides based on the unique mass relationships between parent ions of cross-linked peptides and their fragment ions to obtain an MS/MS result including a list of parent ions corresponding to cross-linked peptide candidates (e.g., the putative or potential identities of the cross-linked peptides being analyzed).

In some embodiments, analysis of the MS/MS data is carried out using the Link-Finder program. Monoisotopic masses and charges of parent ions measured in MS scans for those putative cross-linked peptides identified by the Link-Finder program were subsequently submitted to MS-Bridge to determine cross-linked peptide sequences by mass mapping with a given cross-linker (i.e. DSSO) and protein sequences (see Chu, F.,et al.). For example, one embodiment of the invention further includes mass mapping the MS data using the list of parent ions corresponding to the cross-linked peptide candidates and the MS-cleavable cross-linker againt known protein sequences to obtain an MS result comprising possible cross-linked peptide sequences.

In some embodiments, the mass mapping is carried out using MS-Bridge. The parent mass error for MS-Bridge search was set as ±10 ppm and only one cross-link was allowed in the cross-linked peptides for general search. All of the three types of the cross-linked peptides (Schilling, B., et al.), i.e. inter-linked (type 2), intra-linked (type 1) and dead-end modified (type 0), can be computed and matched in MS-Bridge (see Chu, F.,et al.).

The search results from Link-Finder, Batch-Tag and MS-Bridge programs are integrated together using in-house scripts to compile a list of cross-linked peptides identified with high confidence. The final results were validated manually by examining MS/MS spectra and MS³ spectra respectively.

Synthesis of Two New Enrichable and MS-Cleavable Cross-Linkers to Define Protein-Protein Interactions by Mass Spectrometry

The cross-linking Mass Spectrometry (XL-MS) technique extracts structural information from protein complexes without requiring highly purified samples, crystallinity, or large amounts of material. However, there are challenges to applying the technique to protein complexes in vitro, and those challenges become more daunting with in vivo experiments. Issues include effective detection and identification of cross-linked peptides from complex mixtures. While MS-cleavable cross-linkers facilitate the sequencing and identification of cross-linked peptides, enrichable cross-linkers increase their detectability by allowing their separation from non-cross-linked peptides prior to MS analysis. Although a number of cross-linkers with single functionality have been developed in recent years, an ideal reagent would incorporate both capabilities for XL-MS studies.

Therefore, two new cross-linkers have been designed and prepared that incorporate an azide (azide-A-DSBSO) or alkyne (alkyne-A-DSBSO) to enable affinity purification strategies based on click chemistry. The integration of an acid cleavage site next to the enrichment handle allows easy recovery of cross-linked products during affinity purification. In addition, these sulfoxide containing cross-linking reagents possess robust MS-cleavable bonds to facilitate fast and easy identification of cross-linked peptides using MS analysis. Optimized, gram-scale syntheses of these cross-linkers have been developed and the azide-A-DSBSO cross-linker has been evaluated with peptides and proteins to demonstrate its utility in XL-MS analysis.

In some embodiments, the preparation of two-CID-cleavable lysine cross-linkers, an azide (azide-A-DSBSO) and an alkyne (alkyne-A-DSBSO) are provided.

In some embodiments, initial characterization of azide (azide-A-DSBSO) and an alkyne (alkyne-A-DSBSO) using a model peptide and a model protein are provided.

In some embodiments, while not trivial, the syntheses procedures provided herein have been optimized to make these useful compounds available on multigram scale.

In some embodiments, the azide and alkyne functional groups are suitable for click enrichment strategies.

In some embodiments, the cross-linkers described herein have been utilized in mammalian HEK-293 cells⁶.

In some embodiments, the cross-linkers described herein facilitate the study of the interaction of subunits in the proteasome complex, which is responsible for degradation of ubiquitin tagged proteins.⁶

In some embodiments, the importance of developing XL-MS reagents that are applicable for in vivo studies is significant because protein-protein interactions are involved in most cell function and are not well understood.

Most proteins act in association with other proteins to form protein complexes stably or transiently in cells, and mapping these interactions is essential to understand their cellular functions. Protein complexes represent functional entities that are often difficult to analyze using conventional structural cools clue to their heterogeneous and dynamic nature. Recently, cross-linking Mass Spectrometry (XL-MS) has been recognized as a valuable tool for the structural analysis of protein assemblies, which can be used alone and in combination with other techniques.^(1,2) In addition to in vitro studies, XL-MS approaches have been extended to capture protein interactions in living cells.³

Identification of cross-linked peptides by MS analysis can provide distance constraints to assist computational modeling and yield structural information at amino acid resolution.⁴ The advantages of cross-linking studies include small sample size, robust tolerance for size and environment of the protein complex, instrument accessibility, and the speed of handling and data collection. Although successful, inherent limitations in current XL-MS strategies require further developments to enable MS detection and identification of cross-linked peptides with better efficiency, accuracy, sensitivity and speed. Among various approaches to improve existing XL-MS workflow,⁵ developing new cross-linking reagents holds the greatest promise towards the ultimate goal of mapping protein-protein interactions in living cells at the systems level.

In some embodiments, the chemical synthesis of two new cross-linking agents is provided whose effectiveness has recently been demonstrated for in vivo protein-protein analysis.⁶

Unambiguous identification of cross-linked peptides can be greatly facilitated by the introduction of a MS cleavable bond in a cross-linking reagent, which can fragment during collision induced dissociation (CID) prior to peptide backbone breakage.⁷ In some embodiments, successful development of a new class of robust MS-cleavable reagents that contain labile C—S sulfoxide bonds (e.g. DSSO (disuccinimidylsulfoxide), FIG. 13) is provided, which enables fast and accurate identification of cross-linked peptides using liquid chromatography-multistage tandem mass spectrometry analysis (LC/MS^(n)).^(8,9)

In some embodiments, with DSSO as an example, the new XL-MS workflow provided herein involves protein DSSO cross-linking, trypsin digestion of cross-linked proteins, and LC/MS^(n) analysis of resulting peptide mixtures. During MS^(n) analysis, the cross-linked peptides are first detected in MS¹ and selected for subsequent MS² analysis. The CID-fragmentation site, i.e. one of the C—S sulfoxide bonds, is selectively fragmented in MS², allowing the physical separation of the two DSSO cross-linked peptide constituents for subsequent sequencing. The resulting peptide fragments in MS² are then analyzed in MS for unambiguous identification. The integration of these three types of MS data (MS¹, MS², MS³) enables simplified analysis of DSSO cross-linked peptides with improved speed and accuracy. This strategy has been demonstrated to be effective in the structural analysis of purified protein complexes in vitro.⁴

The analytical problem with effectively detecting and identifying cross-linked peptides becomes much more daunting with large, complex protein assemblies and especially when studying protein-protein interactions in living cells. A strategy to improve the sensitivity and efficiency of XL-MS analysis is to incorporate an affinity purification handle into the cross-linker itself.

To this end, in some embodiments, an azide-tagged cross-linking reagent is provided that allows the incorporation of an affinity purification handle based on click chemistry for enriching cross-linked peptides prior to MS analysis, thus improving their detection and identification.¹⁸ In comparison to other enrichment handles incorporated in cross-linking reagents,¹⁰ the azide group is advantageous as it is small, bioorthogonal, and click chemistry has been proven effective in enriching biological samples for various proteomic analyses including cross-linking studies.¹¹

In some embodiments, in order to combine these unique features in a multifunctional cross-linking reagent that can advance current XL-MS workflow for studying protein-protein interactions in vivo as well as in vitro, a new class of low molecular weight, membrane permeable, enrichable and MS-cleavable cross-linkers is provided.

In some embodiments, in order to explore the flexibility of using azide-alkyne click chemistry in the XL-MS workflow, two new cross-linkers, i.e., azide-tagged and an alkyne-tagged reagents were designed and synthesized as presented in FIG. 14. The structure of azide-A-DSBSO (azide-tagged, acid-cleavable disuccinimidyl-bissulfoxide) 3 incorporates a number of important design elements (FIG. 14).

The N-hydroxysuccinimidyl (NHS) esters are designed to react with lysine side chains thus cross-linking the proteins in the complex. The sulfoxide groups provide MS-cleavable bonds, and because only one side of each sulfoxide has β-hydrogen atoms, the elimination must take place regioselectively at the outer c-s bond. The design incorporates an

azide functional group to be used in click reactions with strained alkynes or in a coppe(r)-catalyzed azide-alkyne cycloaddition (CuAAC).¹²

The click and CuAAC reactions enable several strategies for affinity purification, including direct coupling with alkyne or azide-functionalized beads or by linking with common affinity ligands such as biotin.¹¹ Finally, the azide portion of the molecule is joined to the cross-linker with an acid labile acetal bond, which can be cleaved under aqueous acidic conditions to facilitate selective elution from an affinity column.

The same elements are incorporated into the alkyne-A-DSBSO (alkyne-tagged, acid-cleavable disuccinimidyl-bissulfoxide) 4, except that the azide functional group

has been exchanged for the complementary alkyne. One other design feature is that both of these cross-linkers, prior to the introduction of the sulfoxides, are achiral and exist as single stereoisomers (FIG. 14).

This feature offers considerable simplification in the preparation and analysis of the synthetic intermediates, and decreases the chance of any stereoselective behavior in the crosslinking environment. These reagents have been under investigation for several years in our program and their applications in mapping protein-protein interactions at the systems level in living cells were recently described.⁶ In this report, the syntheses of these reagents are described in full along with foundational studies on the cross-linking effectiveness and LC/MS^(n) sequencing.

Synthesis of the Cross-Linkers 3 and 4

The original synthesis of azide-A-DSBSO 3 began with pentaerythritol (5) and is presented in FIG. 15. Selective protection of 5 (2,2-bis(hydroxymethyl)propane-1,3-diol) as cyclohexanone acetal 6 ((1,5-dioxaspiro[5.5]undecane-3,3-diyl)dimethanol) represented an improvement of the literature procedure.¹³ Mesylation followed by displacement with potassium thioacetate produced the bis-thioacetate 8 (S,S′-((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene)) diethanethioate) in good overall yield. All three intermediates, 6, 7 ((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene) dimethanesulfonate) and 8, were crystalline solids that were isolated and purified on multi-gram scale without chromatography. Thioacetate methanalysis and Michael addition of 8 into methyl acrylate was accomplished in a single step in the presence of triethylamine and methanol. The key intermediate 9 (dimethyl 3,3′-(((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene))bis(sulfanediyl))dipropionate) was isolated in nearly quantitative yield and used without further purification. Careful hydrolysis of the cyclohexanone acetal using In(OTf)₃ catalysis produced 86% of the diol 10 (dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate) and 8% recovered starting material, which were separated by chromatography. Incomplete hydrolysis of the acetal was a recurring problem in this step when using

Brønsted or Lewis acids in refluxing solvent, which required isolation and recycling of a small amount of the recovered acetal 9. By carefully optimizing the catalyst quantity, time, and temperature in microwave reaction conditions the conversion to diol 10 could be pushed to completion with isolated yields of ˜94%. Diol 10 is a key intermediate in the synthesis, and it is the branch point for the preparation of the azide cross-linker 3 and the alkyne cross-linker 4. It was prepared in five steps following this route in 64% overall yield with only one chromatographic purification.¹⁴

The remainder of the synthesis of azide cross-linker 3 is outlined in FIG. 15. The diol 10 was reacted with 5-azidopentan-2-one (11)¹⁵ with acid catalysis using a Dean-Stark trap to remove water. The acetal 12 (dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate) was isolated in 77% yield by chromatography. The NHS esters were introduced in two steps: hydrolysis of the methyl ester and coupling with N-hydroxysuccinimide using EDC-HCl in dimethylformamide (DMF). In FIG. 15, 13 is 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionic acid. The overall yield was typically around 60% and the bis-NHS ester 14 (bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate) was isolated with chromatography. The final oxidation was carried out with meta-chloroperoxybenzoic acid (m-CPBA); the oxidant was added in aliquots and conversion was monitored by ESI-MS until the starting material and monosulfoxide were no longer present. Azide cross-linker 3 was isolated by extraction. This route produced several grams of the cross-linker 3 in ca. 18% overall yield for the sequence.¹⁴

In the course of in vivo studies,⁶ it was found that the azide 3 cross the membrane and produced cross-links in targeted protein complexes.⁶ The studies require a large excess of cross-linker, and led to an ongoing demand for more material. Although the original optimized synthesis in FIG. 15 was effective, it did require nine steps. A shorter route was developed that incorporated several improvements in the individual transformations and avoided the use of protecting groups. The new route is presented in FIG. 16.

The new route (FIG. 16) begins with the commercially available and inexpensive dibromide 15 (2,2-bis(bromomethyl)propane-1,3-diol) and thiol 16 (methyl 3-mercaptopropanoate). Direct alkylation with K₂CO₃ in DMF generate the key intermediate 10 in a single step. Diol 10 could be purified by chromatography on silica gel to produce 75% of pure 10, but the crude product was carried on in the sequence. By comparison to the original route (FIG. 15), this synthesis was carried out using the Noyori protocol,¹⁶ which was found to be more reliable than the original acid-catalyzed method. Diol 10 was silylated and then combined with ketone 11 in the present of TMSOTf to give acetal 12 in 65% overall yield. Hydrolysis of the dimethyl ester 12 used LiOH as before. The bis-NHS ester 14 was prepared using in situ generated TFA-NHS,¹⁷ which lead to similar overall yields but shorter reaction times, fewer side products, and a more reliable purification. Finally, oxidation to the bis-sulfoxide as previously described gave azide 3. The new route requires only six steps, three chromatographic purifications, and led to an overall yield of 38%.¹⁴ It is more convenient and reliable than the prior route and has been used to produce multiple grams of azide-A-DSBSO 3.

The 5-azidopentan-2-one was initially prepared by the alkylation of commercially available bromide 18 with NaN₃.¹⁵ The very high cost of bromide 18 led us to develop a more economical approach starting with lactone 17 (3-acetyldihydrofuran-2(3H)-one) (FIG. 17). The lactone 17 was treated with HBr to generate the required 5-bromopentan-2-one (18). The standard displacement with sodium azide gave the designed ketone 11 in good overall yield. Scaling up the synthesis of azide-A-DSBSO 3 required a significant quantity of the volatile azide 11, and the starting with lactone 17 was both effective and economical.

The alkyne 4 was prepared from diol 10 using a very similar route (FIG. 18). The acetal 19 (dimethyl 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate) was formed from 5-hexyn-2-one and the diol under Dean-Stark conditions. The dimethyl ester was hydrolyzed to a diacid using LiOH, and the di-NHS ester was prepared using TFA-NHS reagent.¹⁷ Di=NHS ester 20 (bis(2,5-dioxopyrrolidin-1-yl)3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate) was isolated in 60% yield using this method. The same compound was also prepared using an EDCI coupling, but the yield was lower and the purification was more difficult. The m-CPBA oxidation was conducted as described for the azide substrate to give the Alkyne-A-DSBSO 4. The route required only four steps from diol 10 and made cross-linker 4 available on gram scale.

MSn Analysis of Azide-A-DSBSO Cross-Linked Ac-Myelin Peptide

Given the similarity of cleavable C—S bonds in azide-A-DSBSO and DSSO, it was anticipated that azide-A-DSBSO cross-linked peptides would display comparable fragmentation characteristics to DSSO cross-linked peptides (FIG. 19A).⁴ In such experiments, MS² produces peptide fragments that are modified with remnant portions of the cross-linking reagents. These remnants are not identical thus producing two products with a separation of 254 Da, the α_(A) and the α_(T) fragments. The α_(A) fragment has an alkene group, while the other half of the cleaved linker results in a terminal thiol group (after hydrolysis of the sulfenic acid intermediate). Although azide-A-DSBSO contains four C—S bonds due to the presence of two sulfoxide groups, the two central C—S bonds cannot undergo fragmentation due to the lack of β-hydrogens. Therefore, only the two C—S bonds closer to cross-linked residues are expected to fragment during MS².

To examine MS² fragmentation patterns of azide-A-DSBSO cross-linked peptides during MS^(n) analysis, the model peptide Ac-myelin was first cross-linked and analyzed. MS¹ analysis detected azide-A-DSBSO cross-linked Ac-myelin (α-α) homodimer at four different charge states (m/z 501.41⁶⁺, 601.4⁵⁺, 751.62⁴⁺, 1001.82³⁺) (FIG. 19B). MS² analyses of inter-linked Ac-myelin homodimer at different charge states yielded the expected fragmentation of two identical inter-linked peptides, i.e. a characteristic fragment pair (α_(A)/α_(T)). As an example, the fragment pair α_(A)/α_(T) detected in MS/MS spectra of the quadruply (m/z 751.62⁴⁺) and sextuply (m/z 501.411⁶⁺) charged interlinked Ac-myelin (α-α) was displayed in FIG. 19C and FIG. 19D, respectively. The results demonstrate that the MS-cleavable C—S bonds in azide-A-DSBSO cross-linked peptides are preferentially fragmented during MS² analysis prior to the breakage of peptide backbones. Similar results were observed with alkyne-A-DSBSO cross-linked Ac-myelin peptide (data not shown) as azide-A-DSBSO and alkene-A-DSBSO are almost identical in structures.

LC/MSn Analysis of DSBSO Cross-Linked Peptides of Cytochrome C After Enrichment

In some embodiments, to demonstrate the applicability of azide-A-DSBSO for XL-MS studies, the model protein cytochrome C was cross-linked with with azide-A-DSBSO. Cytochrome C has been used extensively by us and other groups for evaluating cross-linking reagents because it is a small protein with a high number of lysine residues. Given its success in the past for cross-linking studies,^(4,18) it was decided to use it as the model protein for characterizing our new cross-linking reagent. The resulting cross-linked cytochrome C products were conjugated with BARAC-biotin,¹⁹ affinity purified by binding to Streptavidin beads, and digested with trypsin.

The cross-linked peptides were eluted from the beads with acid, and thus became acid-cleaved products of azide-A-DSBSO cross-linked peptides, i.e., DSBSO cross-linked peptides, which were then subjected to LC/MS^(n) analysis. The general workflow and the structure of the cross-linked peptides leading up to LC/MS^(n) analysis are illustrated in FIG. 20. As illustrated, the acid-cleaved products are the final analytes for LC/MS^(n) analysis. It is noted that the acid-cleaved products of azide-A-DSBSO and alkyne-A-DSBSO cross-linked peptides are the same, because the differentiated group is lost during the acid elution of cross-linked peptides form affinity matrix during enrichment.

Since the cleavable C—S bonds in SDBSO are similar to those in DSSO, the general data analysis work flow for the identification of SDBSO cross-linked peptides by LC/MS^(n) is similar to the analysis of DSSO cross-linked peptides.⁴ There are three types of cross-linked peptides, i.e., dead-end, intra-linked, and inter-linked peptides. Among them, inter-linked peptides provide the most informative structure details for defining protein-protein interaction interfaces. Therefore, in some embodiments, the goal that is most interested is to identify inter-linked peptides between the same and/or different proteins.

As an example, FIG. 21A-FIG. 21D describe a representative MS^(n) analysis of a DSBSO inter-linked cytochrome C peptide (α-β) that was detected as a quadruply charged ion (m/z, 510.0166⁴⁺). As shown MS² analysis resulted in two pairs of peptide fragments (i.e., α_(A)/β_(T) or α_(T)/β_(A)), characteristic fragmentation of inter-linked heterodimeric peptide. Subsequent MS³ analysis of MS² fragment α_(A) (m/z 430.75²⁺) and β_(A) (m/z 489.28²⁺) determined their sequences as K_(A)YPIGTK and M(_(OX))IFAGIK_(A)K respectively, in which K_(A) is modified with the alkene moiety. Integration of MS¹, MS², MS³ results has unambiguously determined this DSBSO cross-linked cytochrome C peptide as [⁷⁴KYIPGTK⁸⁰ inter-linked to ⁸¹M(_(OX))IFAGIKK⁸⁸], in which a cross-link was formed between K74 and K87 in cytochrome C.

In total, LC/MS^(n) analysis of enriched cross-linked cytochrome C identified 7 unique inter-linked peptides. TABLE 7 provides summary of Unique Inter-linked Peptides Identified from Azide-A-DSBSO Cross-linked CytC. In addition, 11 unique dead-end and 5 unique intralinked cytochrome C peptides were identified since all types of cross-linked peptides can be selectively enriched (data not shown). The results are comparable to those obtained using DSSO cross-linking,⁴ demonstrating the effectiveness of azide-A-DSBSO based XL-MS strategy. Although it is not necessary to enrich cross-linked peptides for simple proteins like cytochrome C, it is evident that such a process is essential for mapping protein interaction interfaces at the systems level.⁶

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General Experimental Details

All chemicals were purchased from Sigma-Aldrich, Acros Organics, Alfa Aesar, TCI, Advanced ChemTech, or Fisher and used without further purification unless otherwise noted. 1,5-Dioxaspiro[5.5]undecane-3,3-diyldimethanol (diol ₆)¹, N-hydroxysuccinimidyl trifluoroacetate², and 5-azido pentanone (azide 11)³ were synthesized according to literature procedure. Ethanol was purchased from Gold Shield. Solvents were of reagent grade and used as without further purification except as follows: N,N-dimethylformamide (DMF), dichloromethane (DCM), and tetrahydrofuran (THF) were degassed and then passed through anhydrous neutral alumina A-2 before use, according to the procedure described by Grubbs.⁴ Methanol was dried over activated 3 Å molecular sieves prior to use. Triethylamine was distilled over calcium hydride and stored over activated 3 Å molecular sieves prior to use. Diisopropylethylamine (DIPEA) was distilled over calcium hydride prior to use. Trifluoroacetic anhydride (TFAA) and trimethylsilyl triflate (TMSOTf) were distilled prior to use. Reported reaction temperatures refer to the temperature of the heating medium. Reactions were performed in flame- or oven-dried glassware under an atmosphere of dry argon using standard Schlenk techniques unless otherwise noted. Room temperature (rt) refers to 25±3° C. Reactions were monitored by thin-layer chromatography (TLC) using EMD Chemicals Inc. silica gel 60 F256 plates. Flash chromatography was performed using Ultra Pure SiliaFlash P60, 230-400 mesh (40-63 μm) silica gel (SiO₂) following the general procedure by Still and co-workers.⁵

Instrumentation

Proton NMR spectra measurements were acquired at 500 MHz and 600 MHz. Carbon NMR spectra were obtained at 125 MHz. Proton NMR chemical shifts (δ) are reported in parts per million (ppm) and referenced to the residual solvent peak at 7.27 ppm for deuterated chloroform (CDCl₃) and 2.50 for deuterated dimethyl sulfoxide (DMSO-d₆). Carbon NMR chemical shifts (δ) are reported in ppm and referenced to the residual solvent peak at 77.23 ppm for deuterated chloroform and 39.52 for deuterated dimethylsulfoxide.⁶ NMR data are reported in the following manner: chemical shift, multiplicity, (s=singlet, d=doublet, t=triplet, q=quartet, quin=quintet, m=multiplet, br=broad, app=apparent), coupling constants (J) in hertz (Hz), and integration. High Resolution Mass Spectrometry (HRMS) accurate mass experiments were performed by the University of California, Irvine mass spectrometry laboratory.

Experimental Procedures. Bis(2,5-dioxopyrrolidin-1-yl)-3,3′-((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylenesulfinyl))dipropanoate (azide-A-DSBSO) (3)

NHS ester 14 (1.21 g, 2.00 mmol) was dissolved in CHCl3 (40 mL), and the reaction mixture was cooled to 0° C. A solution of m-CPBA (0.905 g, 77% mixture with the remainder water, 4.03 mmol) in CHCl₃ (40 mL) was added drop-wise and the reaction mixture was stirred for 10 min. The reaction mixture was diluted with CHCl₃ (100 mL), and then washed with saturated aqueous NaHCO₃ (3×125 mL). The CHCl₃ layer was dried over MgSO₄, filtered, and concentrated to afford bis-sulfoxide 3 as a white solid and mixture of diastereomers (1.13 g, 89%): 1H NMR (500 MHz, DMSO-d6) δ 3.98-3.79 (m, 4H), 3.35 (appar. t, 2H, J=6.8 Hz), 3.29-2.98 (m, 12H), 2.82 (s, 8H), 1.76-1.56 (m, 4H), 1.36 (s, 3H); ¹³C NMR (125 MHz, DMSO-d₆) δ 170.10, 170.08, 167.78, 167.76, 99.18, 99.06, 79.19 (residual CHCl₃), 65.82, 65.4, 65.0, 64.68, 55.03, 54.75, 54.62, 50.82, 46.11, 46.02, 45.73, 45.67, 40.02, 36.43, 36.31, 34.66, 34.60, 25.48, 25.25, 23.21, 23.18, 23.08, 23.04, 22.66, 20.12, 20.06; IR (KBr) 2931, 2850, 2098, 1782, 1739, 1624 cm⁻¹; HRMS (ESI) m/z calcd for C₂₄H₃₃N₅O₁₂S₂Na [M+Na]⁺ 670.1465, found 670.1450.

Bis(2,5-dioxopyrrolidin-1-yl) 3,3′-((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis-(methylenesulfinyl))dipropanoate (alkyne-A-DSBSO) (4)

NHS ester 21 (1.82 g, 3.11 mmol) was dissolved in CHCl₃ (105 mL), and the solution was cooled to 0° C. Next m-CPBA (1.40 g, 77% mixture with the remainder water, 6.24 mmol) was dissolved in CHCl₃ (56.5 mL), then was added drop-wise, and the reaction mixture was stirred for 10 min. The reaction mixture was diluted with CHCl₃ (175 mL), and then washed with saturated aqueous NaHCO₃ (5×40 mL). The CHCl₃ layer was collected, dried over MgSO4, filtered, and concentrated to afford 4 as a white solid and mixture of diastereomers (1.88 g, 98%): 1H NMR (500 MHz, DMSO-d6) δ 4.01-3.79 (m, 4H), 3.32, (s, 1H), 3.29-2.97 (m, 10H), 2.82 (s, 8H), 2.75 (s, 1H), 2.26-2.19 (m, 2H), 1.94-1.85 (m, 3H), 1.37 (s, 3H); ¹³C NMR (125 MHz, DMSO-d₆) δ 170.1, 167.8, 98.46, 98.36, 84.40, 79.19 (residual CHCl₃), 71.03, 65.8, 65.3, 65.0, 64.59, 55.1, 54.7, 54.5, 46.00, 45.69, 45.63, 40.12, 40.02, 36.7, 36.37, 36.27, 25.46, 23.20, 23.15, 23.07, 23.01, 19.81, 12.28; IR (thin film) 3294, 2989, 2934, 2877, 2117, 1813, 1782, 1736, 1427, 1365, 1207, 1134, 1088, 1068. 1034 cm⁻¹; HRMS (ESI) m/z calcd for C₂₅H₃₂N₂O₁₂S₂ [M+Na]⁺ 639.1295, found 639.1295.

1,5-Dioxaspiro[5.5]undecane-3,3-diylbis(methylene)dimethanesulfonate (7)

Diol 6 (30.18 g, 139.5 mmol)¹ was dissolved in DMF (420 mL), and triethylamine (78 mL, 560 mmol) was added via syringe. At 0° C., methanesulfonyl chloride (30.0 mL, 388 mmol) was added drop-wise via addition funnel. The solution was gradually warmed to rt, and stirred for 24 h. More DMF (240 mL), triethylamine (38 mL, 270 mmol) and methanesulfonyl chloride (11 mL, 140 mmol) were added at rt and the mixture was stirred another 24 h. The reaction mixture was filtered and the filter cake was rinsed with EtOAc (3×100 mL). Additional EtOAc (500 mL) was added, and the solution was washed with saturated aqueous NaHCO₃ (150 mL). The aqueous layer was back extracted with EtOAc (150 mL), and the combined organic layers were washed with saturated aqueous NaHCO₃ (2×150 mL), water (3×100 mL), and brine (150 mL). The EtOAc layer was dried over MgSO₄, filtered, and concentrated. The crude brown oil was dissolved in CH2Cl2 and concentrated repeatedly until a red solid formed. The red solid was scraped out of the flask and chopped into a fine powder at which point the appearance changed to a light yellow solid. The yellow solid was stirred in 900 mL boiling ether, 125 mL CH₂Cl₂ was slowly added while maintaining a boil and then filtered hot. The clear yellow filtrate was boiled down to 600 mL and then hexanes (100 mL) were added slowly while maintaining a boil. The solution was further boiled down to 600 mL, allowed to cool to room temperature then placed in a freezer overnight. The resulting crystals were filtered, washed 3 times with cold hexanes and dried under high vacuum to afford 7 as off-white long needle shaped crystals (32.17 g, 62%). The mother liquors and hot-filtration materials were purified by column chromatography (step-gradient from 6:4 hexanes:EtOAc to 1:2 hexanes:EtOAc) to afford additional 7 as off-white crystals (15.57 g, 30%): 1H NMR (500 MHz, CDCl₃) δ 4.28 (s, 4H), 3.79 (s, 4H), 3.07 (s, 6H), 1.76-1.66 (m, 4H), 1.51-1.44 (m, 4H), 1.45-1.41 (m, 2H); 13C NMR (125 MHz, CDCl₃) δ 99.4, 68.0, 60.8, 38.4, 37.4, 32.5, 25.6, 22.6; IR (KBr pellet) 2943, 2862, 1354 cm⁻¹; HRMS (ESI) m/z calcd for C₁₃H₂₄O₈S₂Na [M+Na]⁺ 395.0810, found 395.0801.

S,S′-(1,5-Dioxaspiro[5.5]undecane-3,3-diylbis(methylene))diethanethioate (8)

Mesylate 7 (6.38 g, 17.1 mmol) was dissolved in DMF (90 mL). Potassium thioacetate (7.85 g, 68.7 mmol) was added at room temp and the solution was heated to 55° C. for 48 h. The precipitates were filtered off, washed with excess EtOAc, and the filtrate was concentrated to dryness. The red crystalline solid was recrystallized from hexanes (9.82 g in 500 mL) after hot filtration the solution was brought back to a boil (total volume 375 mL). The solution was cooled, placed in the freezer overnight, filtered, and washed with cold hexanes affording 8 as off-white small crystals (3.95 g, 69%). The mother liquors and hot-filtration materials were purified by column chromatography (9:1 hexanes:EtOAc) to afford additional 8 as an off-white solid (1.14 g, 20%): 1H NMR (500 MHz, CDC13) 6 3.65 (s, 4H), 3.09 (s, 4H), 2.37 (s, 6H), 1.75-1.67 (m, 4H), 1.58 (H2O), 1.52-1.44 (m, 4H), 1.40 (app d, J=4.2 Hz, 2H); 13C NMR (125 MHz, CDC13) 6 195.1, 98.7, 65.3, 37.3, 32.6, 31.8, 30.9, 25.80, 22.70; IR (KBr pellet) 2927, 2866, 1693, 1446 cm⁻¹; HRMS (ESI) m/z calcd for C₁₅H₂₄O₄S₂Na [M+Na]⁺ 355.1014, found 355.1020.

Dimethyl 3,3′-((1,5-dioxaspiro[5.5]undecane-3,3-diylbis(methylene))bis(sulfanediyl))-dipropanoate (9)

Thioacetate 8 (3.95 g, 11.9 mmol) was dissolved in MeOH (300 mL), and triethylamine (8.5 mL, 61 mmol) was added. Methyl acrylate (3.20 mL, 36 mmol) was added dropwise via syringe and the solution was stirred at room temp for 6 h. The solution was concentrated, dissolved in CH2Cl2, and concentrated to dryness to afford 9 as a clear light brown oil (4.90 g, 98%): ¹H NMR (500 MHz, CDCl₃) δ 3.73 (s, 4H), 3.71 (s, 6H), 2.82 (t, J=7.4 Hz, 4H), 2.74 (s, 4H), 2.64 (t, J=7.3 Hz, 4H), 1.74 (br s, 4H), 1.51 (t, J=5.4 Hz, 4H), 1.41 (app d, J=4.2 Hz, 2H); ¹³C NMR (125 MHz, CDCl₃) δ 172.5, 98.6, 65.5, 52.0, 38.4, 36.0, 34.9, 32.8, 29.1, 25.8, 22.7; IR (neat) 2947, 2862, 1739, 1439 cm⁻¹; HRMS (ESI) m/z calcd for C₁₉H₃₂O₆S₂Na [M+Na]⁺ 443.1538, found 443.1522.

Dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropanoate (10)

In(OTf)3 Procedure: Ketal 9 (0.202 g, 0.482 mmol) was placed in a microwave tube followed by In(OTf)₃ (0.0079 g, 0.014 mmol), MeOH (1.9 mL), and H₂O (433 mL, 24.0 mmol). The solution was placed in a microwave reactor and heated to 70° C. at 50 psi for 30 min. The solution was concentrated and purified by column chromatography: The solution was concentrated, redissolved in a minimal amount of CDCl₃ and loaded onto a silica gel column of 1.8 cm O.D. packed 12 cm high with a slurry of 20 mL silica in 3:1 Hexanes:EtOAc, and eluted with 100 mL 3:1, 50 mL 2:1, 50 mL 1:1, 100 mL 1:2, 100 mL 1:3 hexanes:EtOAc. After collecting 10 mL fractions; fractions 4-8 were concentrated to afford to afford starting material 9 (0.0175 g, 8.6%) and fractions 24-38 were concentrated to afford 10 as a clear yellow oil (0.140 g, 86%). Characterization data were identical to that of the products using the DOWEX procedure below.

DOWEX Procedure: Ketal 9 (5.07 g, 12.05 mmol) was dissolved in MeOH (150 mL), and DOWEX 50WX8-100 resin (35 g) was added to the solution. After stirring vigorously for 18 h, the reaction mixture was filtered, and the filtrate was concentrated under reduced pressure. The crude oil was purified by column chromatography: A column of 5 cm O.D. packed 16 cm high with a slurry of 200 mL silica was loaded with the crude oil and eluted using 600 mL 3:1, 250 mL 7:3, 250 mL 6:4, 250 mL 1:1, 500 mL 1:2, 250 mL 7:3, 250 mL 8:2 hexanes:EtOAc to afford starting material 9 (0.720 g, 14%) and 10 as a clear yellow oil (2.76 g, 67%): ¹H NMR (500 MHz, CDCl₃) δ 3.72 (s, 6H), 3.67 (d, J=5.7 Hz, 4H), 2.83 (t, J=7.2 Hz, 4H), 2.69 (s, 4H) 2.65 (t, J=7.2 Hz, 4H), 2.39 (br s, 2H); ¹³C NMR (125 MHz, CDCl₃) δ 172.7, 66.1, 52.1, 44.9, 35.1, 34.8, 28.8; IR (neat) 3483, 2924, 1732, 1435 cm−1; HRMS (ESI) m/z calcd for C₁₃H₂₄O₆S₂Na [M+Na]⁺ 363.0192, found 363.0904.

Alkylation Procedure from Diol 15: To a three-necked round bottom flask equipped with an overhead stirrer, a water-cooled condenser, and an argon inlet was added diol 15 (22.0 mL, 197.7 mmol), thiol 16 (17.3 g, 65.9 mmol), potassium carbonate (18.2 g, 131.8 mmol), and DMF (330 mL). The mixture was heated to 40° C. for 24 h, after which the DMF was removed directly from the vessel by vacuum distillation affording diol 10 as a clear colorless oil (22.4 g). Purification of a small sample by column chromatography produced diol 10 in a 75% yield. Characterization data were identical to that of the product using the DOWEX procedure above.

Dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))-bis(sulfanediyl))dipropanoate (12)

Dean-Stark Procedure: Diol 10 (4.58 g, 13.5 mmol) was dissolved in benzene (120 mL). 5-Azido pentanone³ (11) (1.77 g, 13.9 mmol) and CSA (0.314 g, 1.35 mmol) were added to the solution, a Dean-Stark apparatus was attached, and the reaction mixture was heated to 115° C. After 21 h, the reaction mixture was cooled, diluted with EtOAc and partitioned between EtOAc (250 mL) and NaHCO₃ (125 mL). The EtOAc layer was separated, washed with brine (75 mL), dried over MgSO₄, filtered, and concentrated. The crude brown oil was purified by column chromatography: A 6 cm O.D. column packed 15 cm high with 325 mL silica slurry was loaded with the crude product in minimal CH₂Cl₂, eluting 750 mL 4:1, 1000 mL 3:1, 500 mL 7:3 hexanes:ethyl acetate and collecting 125-200 mL fractions. Fractions 8-15 were concentrated affording 12 as a clear light yellow oil (4.78 g, 79%): 1H NMR (500 MHz, CDCl₃) δ 3.78 (d, J=11.9 Hz, 2H), 3.74-3.70 (m, 8H), 3.32 (app t, J=3.4 Hz, 2H), 2.84 (t, J=7.3 Hz, 4H), 2.80 (J=7.3 Hz, 2H), 2.67-2.57 (m, 6H), 1.76-1.73 (m, 4H), 1.39 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 172.4, 99.4, 66.02, 52.0, 51.74, 38.1, 36.0, 35.8, 35.0, 34.9, 29.1, 29.0, 23.1, 20.1; IR (neat) 2954, 2870, 2098, 1739, 1435; cm⁻¹; HRMS (ESI) m/z calcd for C₁₈H₃₁N₃O₆S₂Na [M+Na]⁺ 472.1552, found 472.1556.

Dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))-bis(sulfanediyl))dipropanoate (12)

Noyori Procedure:⁷ To a stirred solution of crude diol 10 from the alkylation procedure (0.756 g, 2.23 mmol) and imidazole (1.04 g, 15.3 mmol) in DMF (28 mL) was added TMSCl (1 M solution in THF, 12.6 mL) resulting in the formation of a yellow solution. After stirring for 12 h, the reaction mixture was quenched with water (150 mL) and extracted with ethyl acetate (3×150 mL). The combined organic portions were washed with water (3×150 mL), dried over anhydrous sodium sulfate, filtered, and concentrated in vacuo to afford the crude TMS ether as an orange oil which was used immediately without further purification: 1H NMR (600 MHz, CDCl3): δ 3.71-3.67 (m, 10H), 2.78 (t, J=7.5 Hz, 4H), 2.61 (t, J=7.5 Hz, 4H), 2.57 (s, 4H), 0.08 (s, 18H).

To a cooled (−78° C.) solution of the crude TMS ether (1.00 g, 2.06 mmol) and azide 113 (0.262 g, 2.06 mmol) was added TMS-OTf (50 μL, 0.1 mmol). The solution was stirred for 12 h, over which the time gradually warmed to room temperature. The reaction was quenched with two drops of pyridine (ca. 100 μL), and the mixture was diluted in ethyl acetate (100 mL). The organic layer was washed with water (2×100 mL) and brine (100 mL), dried over anhydrous sodium sulfate, filtered, and concentrated in vacuo to give crude 12 as a black oil. The crude product was purified by column chromatography (1:3 ethyl acetate:hexanes) to afford 12 as an orange oil (0.651 g, 65% over three steps). ¹H and ¹³C NMR spectra were consistent with those previously reported above.

3,3′-(((2-(3-Azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))-dipropanoic acid (13)

Azide 12 (4.65 g, 10.3 mmol) was dissolved in 4:1 THF:H₂O (67 mL), and LiOH.H₂O (0.913 g, 21.8 mmol) was added to the reaction mixture. After 1 h, additional LiOH.H₂O (0.913 g, 21.8 mmol) was added. The reaction mixture was stirred for an additional 2 h and partitioned between H₂O (50 mL) and hexanes (50 mL). The aqueous layer was acidified to pH 1 with 6 M HCl and extracted with EtOAc (5×25 mL). The combined EtOAc extracts were dried over MgSO4, filtered, and concentrated to afford 13 as a clear, light yellow oil (4.58 g, quant.): ¹H NMR (500 MHz, CDCl₃) δ 11.12 (br s, 2H), 3.78-3.69 (m, 4H), 3.29 (t, J=6.0 Hz, 2H), 2.83-2.76 (m, 6H), 2.67 (dt, J=12.0, 7.1 Hz, 4H), 2.60 (s, 2H), 1.73 (s, 4H), 1.33 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 178.0, 177.9, 99.5, 65.9, 51.6, 38.1, 35.8, 35.6, 34.9, 34.8, 28.6, 28.57, 23.0, 20.0; IR (neat) 3097, 2989, 2098, 1712, 1412 cm−1; HRMS (ES/MeOH) m/z calcd for C₁₆H₂₇N₃O₆S₂Na [M+Na]⁺ 444.1239, found 444.1244.

Bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropanoate (14)

EDC Method: Diacid 13 (2.16 g, 5.12 mmol) was dissolved in DMF (52 mL), and N-hydroxysuccinimide was added (1.413 g, 12.3 mmol). 1-Ethyl-3(3-dimethylaminopropyl)carbodiimide hydrochloride (EDCI.HCl) (2.360 g, 12.3 mmol) was added followed by triethylamine (0.10 mL, 0.71 mmol) and the reaction mixture was stirred for 13 h. The reaction solution was concentrated by half, diluted with EtOAc (50 mL) then washed with sat. ammonium chloride (2×25 mL), sat. NaHCO3 (2×25 mL), water (2×25 mL), and brine (25 mL). The organic layer was dried over Na₂SO₄, filtered, and concentrated. The crude oil was purified by column chromatography by loading onto a column 3.5 cm O.D packed 13 cm high with 100 mL silica slurry in 1:1 hexanes:EtOAc, eluting with 325 mL 1:1, 600 mL 1:2, 200 mL 1:3 hexanes:EtOAc and collecting 175 mL followed by 27 mL fractions. Fractions 9-29 were concentrated affording 14 as a white solid (1.97 g, 62%): ¹H NMR (500 MHz, CDCl₃) δ 3.79 (d, J=11.9 Hz, 2H), 3.73 (d, J=11.9 Hz, 2H) 3.32 (t, J=6.0 Hz, 2H), 3.00-2.78 (m, 18H), 2.66 (s, 2H), 2.05 (acetone), 1.71 (br s, 4H), 1.40 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 169.23, 169.20, 167.3, 99.57, 66.0, 51.76, 38.17, 36.05, 35.89, 35.70, 32.34, 32.25, 28.31, 25.80, 25.56, 23.18, 20.01; IR (KBr) 2931, 2850, 2098, 1782, 1739, 1624 cm⁻¹; LRMS (ES/MeOH) m/z calcd for C₂₄H₃₃N₅O₁₀S₂Na [M+Na]⁺ 638.2, found 638.3.

TFAA Method: To a cooled (0° C.) solution of diacid 13, (2.45 g, 5.81 mmol), N-hydroxysuccinimide (2.68 g, 23.3 mmol), and DIPEA (8.10 mL, 46.4 mmol) in DMF (30 mL) was added TFAA (3.28 mL, 23.3 mmol) dropwise, slowly. The light orange solution was stirred at 0° C. for 3 h, after which the reaction was determined complete by TLC. The reaction mixture was partitioned between ethyl acetate (125 mL) and hydrochloric acid (1 M, 100 mL). The layers were separated, after which the acidic aqueous layer was extracted with ethyl acetate (2×125 mL), and the combined organic layers were washed with sodium bicarbonate solution (1 M, 3×100 mL), water (100 mL), and brine (100 mL). The organic layer was dried over anhydrous sodium sulfate, filtered, and concentrated to a dark oil which was purified by column chromatography (step-gradient from 1:1 hexanes:EtOAc to 1:3 hexanes:EtOAc) affording 14 as a white solid (2.34 g, 66%). ¹H and ¹³C NMR spectra were consistent with those previously reported above.

Dimethyl 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))-bis(sulfanediyl))dipropanoate (19)

Diol 10 (2.21 g, 6.48 mmol) was dissolved in benzene (45 mL). 1-Hexyne-5-one (1.33 g, 13.8 mmol) and CSA (0.152 g, 0.654 mmol) were added to the solution, a Dean-Stark apparatus was attached, and the reaction mixture was heated to 115° C. After 27 h, the reaction mixture was cooled, diluted with EtOAc and partitioned between EtOAc (25 mL) and NaHCO₃ (125 mL). The EtOAc layer was separated, washed with brine (25 mL), dried over MgSO₄, filtered, and concentrated. The crude brown oil was purified by column chromatography using a column 6 cm O.D. packed 15 cm high with 300 mL silica slurried in 4:1 Hexanes:EtOAc. The crude was loaded after dissolution in minimal CH₂Cl₂ and the column was eluted with 250 mL 4:1, 1000 mL 3:1, 500 mL 7:3, 100 mL 65:35 hexanes:EtOAc. After collecting 2×200 mL fractions and 25×100 mL fractions, fractions 8-15 were concentrated affording 19 as a clear light yellow oil (2.08 g, 77%): ¹H NMR (500 MHz, CDCl₃) δ 3.76 (d, J=12.0, 2H), 3.71 (s, 6H), 3.70 (d, J=10.1 Hz, 2H), 2.86-2.77 (m, 6H), 2.66-2.59 (m, 6H), 2.33 (ddd, J=8.2, 6.7, 2.7 Hz, 2H), 1.98-1.93 (m, 3H), 1.39 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 172.40, 172.37, 98.8, 84.5, 68.3, 66.0, 52.0, 38.1, 37.7, 35.9, 35.8, 35.0, 34.9, 29.10, 29.08, 20.1, 12.9; IR (thin film) 3286, 2993, 2951, 2870, 2117, 1739, 1439, 1362, 1250, 1200, 1173, 1134, 1057, 1034; HRMS (ESI) m/z calcd for C₁₉H₃₀O₆S₂ [M+Na]⁺ 441.1382, found 441.1374.

Bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropanoate (20)

Dimethyl ester 19 (0.362 g, 0.864 mmol) was dissolved in 4:1 THF:H₂O (8.0 mL), and LiOH.H₂O (0.125 g, 2.98 mmol) was added to the reaction mixture. After 1 h, additional LiOH.H2O (0.058 g, 1.38 mmol) was added. The reaction mixture was stirred for an additional 2 h and partitioned between H₂O (50 mL) and hexanes (50 mL). The aqueous layer was acidified to pH 1 with 6 M HCl and extracted with EtOAc (5×5 mL). The combined EtOAc extracts were dried over MgSO₄, filtered, and concentrated, dissolved in CH₂Cl₂ and concentrated repeatedly to afford 0.380 g of a light yellow oil, which was used immediately without any further purification: ¹H NMR (500 MHz, CDCl₃) δ 11.20 (br s, 2H), 3.72 (q, 4H, J=9.1 Hz), 2.88-2.76 (m, 6H), 2.73-2.60 (m, 6H), 2.32 (dt, 2H, J=7.9, 2.8 Hz), 1.99-1.90 (m, 3H), 1.39 (s, 3H).

To a portion of the crude diacid intermediate (0.180 g, 0.461 mmol) in CH₂Cl₂ (1.6 mL) and pyridine (0.30 mL, 3.7 mmol) was added N-hydroxysuccinimidyl trifluoroacetate (0.620 g, 2.94 mmol) and the solution was stirred at room temperature for 3 h. The solution was diluted with CH2C12, poured into a separatory funnel, washed with sat. NH₄Cl (5 mL), sat. NaHCO₃ (5 mL), water (5 mL), and brine (5 mL), dried over Na₂SO₄, filtered, and concentrated. The crude product was chromatographed using a column 1.8 cm O.D. packed 12 cm high with a slurry of 20 mL silica and eluting 380 mL 1:2 hexanes:ethyl acetate. After collecting 70 mL followed by 10 mL fractions, fractions 1-13 were concentrated to afford 20 as a white solid (0.162 g, 60%): ¹H NMR (500 MHz, CDCl₃) δ 5.30 (CH₂Cl₂), 3.78 (d, J=12.0 Hz, 2H), 3.71 (d, J=12.5 Hz, 2H), 3.01-2.79 (m, 18H), 2.68 (s, 2H), 2.31 (ddd, J=9.7, 7.6, 2.6 Hz, 2H), 2.00-1.93 (m, 3H), 1.39 (s, 3H); ¹³C NMR (125 MHz, CDCl₃) δ 169.2, 167.3, 98.9, 84.6, 68.3, 66.0, 38.1, 37.4, 35.8, 35.7, 32.3, 32.2, 28.32, 28.26, 25.8, 20.2, 12.9; IR (thin film) 3282, 2947, 2870, 2252, 2114, 1813, 1786, 1739, 1431, 1369, 1250, 1207, 1134, 1068 cm−1; HRMS (ESI) m/z calcd for C₂₅H₃₂N₂O₁₀S₂ [M+Na]⁺ 607.1396, found 607.1388.

Cross-Linking Experiments In Vitro Cross-Linking of Synthetic Peptide Ac-Myelin

Synthetic peptide Ac-myelin was cross-linked with Azide-A-DSBSO in DMSO in a 1:1 molar ratio of peptide to cross-linker at 1 mM in the presence of 1 eq of diisopropylethylamine. Cross-linked peptide solutions were then diluted to 5 pmol/μL in a 3% CAN and 2% formic acid aqueous solution for liquid chromatography multistage tandem mass spectrometry (LC-MS^(n)) analysis.

Cytochrome C

Bovine cytochrome C was solubilized in 50 mM pH 8.0 phosphate buffer at 200 μM and reacted with 20 mM Azide-A-DSBSO dissolved in DMSO at a 1:10 molar ratio of protein to cross-linker for 1 hr at RT. The reaction was quenched with 500 mM NH₄HCO₃ and ultracentrifuged on a 10 kDa NMWL Amicon Ultra centrifugal filters to remove excess cross-linker. To establish the most efficient conditions for biotin conjugation, cross-linked products were washed and concentrated to 450 μM on filter in either 50 mM phosphate buffer or 8 M urea lysis buffer. Various amounts of BARAC were then reacted with the cross-linked cytochrome C in either phosphate or lysis buffer with agitation overnight. The reaction efficiency for each condition was evaluated by immunoblotting, with subsequent experiments carried out in optimal conditions: urea lysis buffer with 100 μM BARAC and agitation overnight. Following conjugation, excess BARAC was removed by ultracentrifugation and washed with 25 mM NH₄HCO₃. Biotin-conjugated cytochrome C was incubated with high-capacity Streptavidin beads and then digested on-bead with 1% trypsin (w/w) or 5% chymotrypsin (w/w) following reduction and alkylation of cysteine residues in 5 mM DTT at 56° C. and 10 mM chloroacetamide at RT, respectively. After digestion, non-cross-linked peptides were extracted and analyzed by LC-MS^(n); cross-linked peptides bound to streptavidin beads were eluted from beads by acid cleavage in 20% FA, 10% ACN solution prior to LC-MSn analysis.

Analysis of Cross-Linked Peptides by LC-MSn

Most of the enriched cross-linked peptides were analyzed by LC-MS^(n) using an LTQ-Orbitrap XL mass spectrometer (Thermo Scientific, San Jose, Calif.) coupled on-line with either an Eksigent NanoLC system (Dublin, Calif.), or EASY-nLC-1000 (Thermo Scientific, San Jose, Calif.). A few of cross-linked samples from intact cells were analyzed using an Orbitrap Elite mass spectrometer (courtesy of Thermo Scientific Demo Lab, San Jose, Calif.) coupled on-line with an EASY-nLC 1000 (Thermo Scientific). LC/MS^(n) data acquisition and analysis were as described.⁸ Only ions with 3+ or higher in the MS 1 scan were selected for MS2 analysis.

Identification of Cross-Linked Peptides by Database Searching

Due to the similarity between DSBSO and DSSO, the general data analysis workflow for the identification of DSBSO inter-linked peptides by LC/MS^(n) is the same as the analysis of DSSO cross-linked peptides.^(8,9) Using the Batch-Tag software within a developmental version of Protein Prospector (v5.10.10, University of California San Francisco), MS2 and MS3 spectra were searched against a decoy database consisting of a normal Swissprot database concatenated with its randomized version (SwissProt.2013.3.1.random.concat with a total of 454,402 protein entries). The mass tolerances for parent ions and fragment ions were set as ±20 ppm and 0.6 Da respectively. Trypsin was set as the enzyme with three maximum missed cleavages allowed. Cysteine carbamidomethylation was set as a constant modification. Protein N-terminal acetylation, asparagine deamidation, N-terminal conversion of glutamine to pyroglutamic acid, and methionine oxidation were selected as variable modifications. Similar to DSSO cross-linked peptides, DSBSO cross-linked peptides display unique and characteristic MS2 fragmentation patterns corresponding to their cross-linking types. Therefore, three additional defined modifications on uncleaved lysines and free protein N-terminus were chosen: alkene (C₃H₂O, +54 Da), sulfenic acid (C₃H₄O₂S, +254 Da), and unsaturated thiol (C₃H₂SO, +236 Da). These are modifications resulting from CID-induced cleavage of the DSBSO cross-linked peptides. The in-house program Link-Hunter is a revised version of the previously written Link-Finder program, designed to automatically validate and summarize cross-linked peptides based MSn data and database searching results as previously described.^(8,9) In addition to checking MS2 spectra for predicted patterns, Link-Hunter automatically correlates sequence data from MS3 to MS2 and MS1 parent masses, reports identified inter-linked peptides with two associated sequences.

REFERENCES—2

-   1. M. C. Murguía, S. E. Vaillard, and R. J. Grau, SYNTHESIS-S, 2001,     7, 1093-1097. -   2. N. M. Leonard, J. Brunckova, J. Org. Chem. 2011, 76, 9169-9174. -   3. Y. Ma, Heteroatom Chem., 2002, 13, 307-309. -   4. B. Pangborn, M. A. Giardello, R. H. Grubbs, R. K. Rosen,     and F. J. Timmers, Organometallics, 1996, 15, 1518-1520. -   5. W. C. Still, M. Kahn, and A. Mitra, J. Org. Chem., 1978, 43,     2923-2925. -   6. G. R. Fulmer, A. J. M. Miller, N. H. Sherden, H. E. Gottlieb, A.     Nudelman, B. M. Stoltz, J. E. Bercaw, and K. I. Goldberg,     Organometallics, 2010, 29, 2176-2179. -   7. T. Tsunoda, M. Suzuki, and R. Noyori, Tetrahedron Lett., 1980,     21, 1357-1358. -   8. Kao, A. Randall, Y. Yang, V. R. Patel, W. Kandur, S. Guan, S. D.     Rychnovsky, P. Baldi, and L. Huang, Mol. Cell. Proteomics MCP, 2012,     11, 1566-1577. -   9. Kao, C. Chiu, D. Vellucci, Y. Yang, V. R. Patel, S. Guan, A.     Randall, P. Baldi, S. D. Rychnovsky, and L. Huang, Mol. Cell.     Proteomics MCP, 2011, 10, M110.002212.

A New In Vivo Cross-Linking Mass Spectrometry Platform to Define Protein-Protein Interactions in Living Cells

Protein-protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, in some embodiments, a new in vivo cross-linking mass spectrometry platform that couples a novel membrane-permeable, enrichable, and MS-cleavable cross-linker with multistage tandem mass spectrometry is provided. In some embodiments, this strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells and thus enables the determination of protein interaction interfaces. In some embodiments, the utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and the targeted protein complex level. In some embodiments, a general approach for studying in vivo PPIs is disclosed. Also provided is a solid foundation for future studies toward the complete mapping of PPI networks in living systems.

In some embodiments, a new and general XL-MS workflow based on Azide-A-DSBSO for studying PPIs in living cells is provided. This new XL-MS workflow differs from existing approaches by its collective abilities allowing (i) effective protein cross-linking in vivo to capture authentic protein interactions, (ii) selective enrichment of cross-linked proteins and peptides to improve their detection, (iii) simplified and unambiguous identification of cross-linked peptides by MSn, and (iv) direct coupling with affinity purification of in vivo cross-linked protein complexes to study their interactions.

In comparison to existing reagents for in vivo studies (24), the integration of several unique features (i.e. small size, proper spacer length, bio-orthogonal affinity handle, robust MS-cleavable bonds, and acid cleavage site) makes Azide-A-DSBSO a much more attractive reagent for defining protein-protein interactions in cells.

Apart from mapping PPIs at the proteome level, successful coupling was achieved of Azide-A-DSBSO-based XL-MS strategy with HB-tag-based affinity purification to delineate the in vivo subunit connectivity of human proteasome complexes for the first time. In some embodiments, this work expands the utility of previously developed cross-linking methodologies such as the QTAX (quantitative analysis of tandem affinity purified in vivo cross-linked (x) protein complexes) strategy in studying in vivo interaction networks of protein complexes beyond the identification of interacting partners (12, 13).

Interestingly, seven out of eight identified pair-wise interactions corroborated well with previous in vitro XL-MS studies of yeast proteasome complexes (19, 20, 36), suggesting that interaction similarity exists between orthologs as well as between in vivo and in vitro proteasome structures.

In this work, the close association between Rpt3 and Rpt6 through the identification of two interlinked peptides at their N-terminal (Rpt3:K80-Rpt6:K55) and central (Rpt3:K238-Rpt6:K222) regions was further confirmed. In addition, the identified contacts between the N termini of Rpt6 and Rpn11, as well as Rpn2, correlate with the electron microscopy structures of yeast proteasomes in which the N-terminal sequences of Rpt3 and Rpt6 form a coil structure for Rpn2 and the lid subcomplex to attach to the base (50, 51).

Moreover, a novel interaction between a3 and Rpt6 identified here implies the intimate relationship of Rpt6 and the 20S α ring. It is worth noting that the identification of these in vivo proteasome subunit contacts was possible only when HB-based affinity purification was incorporated into the workflow, indicating the necessity of targeted analysis for profiling PPIs of protein complexes in cells.

Importantly, our results have proven the feasibility of the Azide-A-DSBSO based XL-MS strategy for such targeted analysis, demonstrating a unique capability that current strategies do not possess. Although other proteasome components were captured and identified from affinity purified Azide-A-DSBSO cross-linked Rpn11-HB or HB-Rpt6 containing proteasome complexes (data not shown), it appears that direct interactions of protein baits are enriched, as eight of the interactions identified were directly with Rpt6.

Although additional baits would be needed to generate a more comprehensive in vivo subunit topology map of the proteasome complex, this would be advantageous when only the direct binding partner needs to be identified. Collectively, this work represents a significant step toward a full understanding of the in vivo PPIs of protein complexes.

Thus, in some embodiments, successful development was achieved of a new, versatile, and general XL-MS workflow for mapping PPIs at both the proteome scale and the targeted protein complex level, representing a technological advancement in defining protein interactions in living systems.

In comparison to previous AP-MS and quantitative tandem affinity purification studies relying on multiple reciprocal purifications and/or existing PPI databases for interaction validation and the construction of in silico interaction network maps (2, 13, 14, 52), our new in vivo XL-MS strategy allows the identification of direct protein interaction contacts for generating interaction networks experimentally.

In addition, this information can be used for determining protein structural topologies in future studies. In combination with stable isotope labeling (53) and cross-linking chemistry targeting other residues such as acidic residues (54), new reagents can be further developed to describe PPI dynamics in cells. The potential of this technology is enormous, and with improvements in instrumentation and sample preparation, a vast variety of unexplored biological applications can be envisioned.

Protein-protein interactions (PPIs)1 play a key role in defining protein functions in biological systems. Aberrant PPIs can have drastic effects on biochemical activities essential to cell homeostasis, growth, and proliferation, and thereby lead to various human diseases (1). Consequently, PPI interfaces have been recognized as a new paradigm for drug development. Therefore, mapping PPIs and their interaction interfaces in living cells is critical not only for a comprehensive understanding of protein function and regulation, but also for describing the molecular mechanisms underlying human pathologies and identifying potential targets for better therapeutics.

Several strategies exist for identifying and mapping PPIs, including yeast two-hybrid, protein microarray, and affinity purification mass spectrometry (AP-MS) (2-5). Thanks to new developments in sample preparation strategies, mass spectrometry technologies, and bioinformatics tools, AP-MS has become a powerful and preferred method for studying PPIs at the systems level (6-9). Unlike other approaches, AP-MS experiments allow the capture of protein interactions directly from their natural cellular environment, thus better retaining native protein structures and biologically relevant interactions. In addition, a broader scope of PPI networks can be obtained with greater sensitivity, accuracy, versatility, and speed. Despite the success of this very promising technique, AP-MS experiments can lead to the loss of weak/transient interactions and/or the reorganization of protein interactions during biochemical manipulation under native purification conditions. To circumvent these problems, in vivo chemical cross-linking has been successfully employed to stabilize protein interactions in native cells or tissues prior to cell lysis (10-16).

The resulting covalent bonds formed between interacting partners allow affinity purification under stringent and fully denaturing conditions, consequently reducing nonspecific background while preserving stable and weak/transient interactions (12-16). Subsequent mass spectrometric analysis can reveal not only the identities of interacting proteins, but also cross-linked amino acid residues. The latter provides direct molecular evidence describing the physical contacts between and within proteins (17).

This information can be used for computational modeling to establish structural topologies of proteins and protein complexes (17-22), as well as for generating experimentally derived protein interaction network topology maps (23, 24). Thus, cross-linking mass spectrometry (XL-MS) strategies represent a powerful and emergent technology that possesses unparalleled capabilities for studying PPIs.

Despite their great potential, current XL-MS studies that have aimed to identify cross-linked peptides have been mostly limited to in vitro cross-linking experiments, with few successfully identifying protein interaction interfaces in living cells (24, 25). This is largely because XL-MS studies remain challenging due to the inherent difficulty in the effective MS detection and accurate identification of cross-linked peptides, as well as in unambiguous assignment of cross-linked residues. In general, cross-linked products are heterogeneous and low in abundance relative to non-cross-linked products. In addition, their MS fragmentation is too complex to be interpreted using conventional database searching tools (17, 26). It is noted that almost all of the current in vivo PPI studies utilize formaldehyde cross-linking because of its membrane permeability and fast kinetics (10-16). However, in comparison to the most commonly used amine reactive NHS ester cross-linkers, identification of formaldehyde cross-linked peptides is even more challenging because of its promiscuous nonspecific reactivity and extremely short spacer length (27). Therefore, further developments in reagents and methods are urgently needed to enable simple MS detection and effective identification of in vivo cross-linked products, and thus allow the mapping of authentic protein contact sites as established in cells, especially for protein complexes.

Various efforts have been made to address the limitations of XL-MS studies, resulting in new developments in bioinformatics tools for improved data interpretation (28-32) and new designs of cross-linking reagents for enhanced MS analysis of cross-linked peptides (24, 33-39). Among these approaches, the development of new cross-linking reagents holds great promise for mapping PPIs on the systems level. One class of cross-linking reagents containing an enrichment handle have been shown to allow selective isolation of cross-linked products from complex mixtures, boosting their detectability by MS (33-35, 40-42). A second class of cross-linkers containing MS-cleavable bonds have proven to be effective in facilitating the unambiguous identification of cross-linked peptides (36-39, 43, 44), as the resulting cross-linked products can be identified based on their characteristic and simplified fragmentation behavior during MS analysis. Therefore, an ideal cross-linking reagent would possess the combined features of both classes of cross-linkers. To advance the study of in vivo PPIs, a new XL-MS platform based on a novel membrane-permeable, enrichable, and MS-cleavable cross-linker, Azide-A-DSBSO (azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide), and multistage tandem mass spectrometry (MS^(n)) was developed. This new XL-MS strategy has been successfully employed to map in vivo PPIs from mammalian cells at both the proteome scale and the targeted protein complex level.

Developing a New In Vivo XL-MS Platform for Mapping PPIs in Living Cells

In order to establish a robust in vivo XL-MS workflow, in some embodiments, the design and synthesis of a novel cross-linking reagent, Azide-A-DSBSO is provided (FIG. 22). The scheme shown in FIG. 22 is similar to the scheme shown in FIG. 15. This multifunctional cross-linker combines the unique features of both enrichable (i.e. azide disuccinimidyl glutarate) (35) and MS-cleavable (i.e. DSSO) cross-linkers previously developed in our lab (36). Azide-A-DSBSO is membrane permeable and has a spacer length of ˜14 Å. In addition, it carries a bio-orthogonal azide tag that functions as an enrichment handle permitting selective isolation of cross-linked proteins and peptides through azide-based conjugation chemistry and subsequent affinity purification (35). The incorporation of an acid-cleavable site adjacent to the azide tag facilitates the purification and recovery of cross-linked peptides. Moreover, the integration of two symmetric sulfoxide groups in the spacer region of Azide-A-DSBSO results in robust MS-cleavable bonds that enable fast and unambiguous identification of cross-linked peptides via MSn analysis (20, 36). Together, these features make Azide-A-DSBSO an ideal reagent for studying PPIs, especially from living cells.

Bovine cytochrome C (>95% purity) was purchased from Sigma Aldrich (St. Louis, Mo.). Amicon Ultra 100-kDa, 30-kDa, and 10-kDa NMWL centrifugal filters were purchased from EMD Millipore (Billerica, Mass.). LaminA/C antibody was purchased from Cell Signaling Technology, Inc. (Danvers, Mass.). Calnexin and GAPDH antibodies were purchased from Santa Cruz Biotechnology (Dallas, Tex.). Streptavidin agarose resin, high-capacity streptavidin agarose resin, HRP-conjugated streptavidin, and Super Signal West Pico chemiluminescent substrate were purchased from Thermo Scientific (Rockford, Ill.). Sequencing-grade trypsin was purchased from Promega Corp. (Madison, Wis.). Endoproteinase Lys-C was purchased from WAKO Chemicals (Osaka, Japan). TPCK-treated trypsin was purchased from Worthington Biochemical Corp (Lakewood, N.J.). All other general chemicals for buffers and culture media were purchased from Fisher Scientific or VWR International (Radnor, Pa.).

The synthesis and characterization of the Azide-A-DSBSO cross-linker are described in Ref. 55. The simplified scheme is depicted in FIG. 22. BARAC reagent was synthesized as described elsewhere (45).

In some embodiments, there are nine steps in the general Azide-A-DSBSO-based XL-MS workflow for mapping in vivo PPIs in mammalian cells illustrated in FIG. 23. As shown, in vivo Azide-A-DSBSO cross-linking is first carried out in intact human cells (e.g. HEK 293) (step 1), which are then lysed under fully denaturing conditions (e.g. 8 m urea) to effectively solubilize cross-linked proteins (step 2). To map PPIs on the global scale (path I), the Azide-A-DSBSO cross-linked proteins in cell lysates are conjugated with a biotin-tagged strained alkyne (i.e. BARAC) through copper-free click chemistry (step 3) (47). The resulting biotinylated cross-linked proteins are then enriched via binding to streptavidin resin (step 4). After removal of the non-cross-linked proteins, bound proteins are directly digested on beads (step 5). The biotin-tagged cross-linked peptides are separated from non-cross-linked peptides, as only cross-linked peptides remain bound to streptavidin beads while other peptides are released to the supernatant during digestion. The bound cross-linked peptides are eluted from streptavidin beads by acid cleavage and become the acid-cleaved products of Azide-A-DSBSO peptides, that is, DSBSO cross-linked peptides (step 6) for subsequent LC-MSn analysis (step 7). The presence of an acid cleavage site in Azide-A-DSBSO not only improves enrichment selectivity, but also facilitates subsequent MS analysis by serving to remove the conjugated enrichment handle to yield a smaller mass tag (˜308 Da) on cross-linked peptides. The analysis of LC-MSn data to identify cross-linked peptides (step 8) is similar to that described elsewhere (20, 36). Finally, the identified interlinked peptides can be used to generate an experimentally derived in vivo cross-linked protein-protein interaction network (step 9).

In addition to mapping PPIs in cells at the proteome scale, in some embodiments, the same strategy can be modified to study in vivo PPIs of protein complexes (FIG. 23, path II). In this workflow, HB-tag-based tandem affinity purification under fully denaturing conditions is implemented to enable the effective purification of in vivo cross-linked protein complexes as previously reported (12-15, 48). This step is crucial for enhancing the sensitivity and selectivity of subsequent analyses of the selected protein complexes. As shown in FIG. 23, after in vivo cross-linking of 293 cells stably expressing an HB-tagged proteasome subunit (e.g. Rpn11-HB), affinity purification of cross-linked HB-tagged protein complexes is carried out through binding first to Ni2+-Sepharose resins, and then to streptavidin beads (step 3′). In some embodiments, the proteins bound to streptavidin beads are directly conjugated with BARAC (step 4′), on-bead digested, and eluted and analyzed via LC-MSn similar to the corresponding steps in path I (steps 5-9).

Selective Enrichment of Azide-A-DSBSO Cross-Linked Peptides

SDS-PAGE and Immunoblotting Analysis was performed by separating protein samples via SDS-PAGE and either stained using Coomassie Blue or transferred to a PVDF membrane and analyzed via immunoblotting. Biotin-conjugated proteins and HB-tagged proteins were detected by streptavidin-HRP conjugate. Cross-linked and non-cross-linked Rpn11-HB and HB-Rpt6 were also detected with streptavidin-HRP conjugate. Lamin A/C, calnexin, and GAPDH were detected using specific primary antibodies and either rabbit or mouse secondary HRP-conjugated antibody. Biotin-conjugated peptides were blotted onto nitrocellulose membrane and detected with streptavidin-HRP conjugate.

One of the key steps in the Azide-A-DSBSO cross-linking strategy is the selective enrichment of cross-linked products. This is achieved by incorporating an affinity tag (e.g. biotin tag) to Azide-A-DSBSO cross-linked products through azide-based conjugation chemistry. Although both copper-catalyzed click chemistry and Staudinger ligation were effective, they have proven to be technically challenging (35). In order to develop a more robust methodology, a copper-free click chemistry reaction using a biotin-tagged strained alkyne BARAC was adopted (47). The tests using Azide-A-DSBSO cross-linked standard protein cytochrome C showed that copper-free conjugation was efficient in both phosphate buffer and buffers containing 8 m urea (FIG. 27A & FIG. 27B), well suited to our goal of capturing protein interactions in living cells using denaturing buffer. Our results suggest that relative to other azide-based conjugation chemistry methods (35), copper-free chemical conjugation is simpler, more efficient, easier in terms of sample handling, and less labor intensive.

Identification of Azide-A-DSBSO Cross-Linked Peptides via LC-MSn

In vitro cross-linking, biotin conjugation, and enrichment of azide-A-DSBSO cross-linked cytochrome C was performed by azide-A-DSBSO cross-linking of bovine cytochrome C was similar to that described elsewhere (35). The reaction was quenched with 500 mm NH4HCO3, and samples were ultracentrifuged on 10-kDa NMWL Amicon Ultra centrifugal filters to remove excess cross-linker. Various amounts of BARAC were then reacted with the cross-linked cytochrome C in either phosphate or 8 m urea lysis buffer with agitation overnight. The reaction efficiency for each condition was evaluated via immunoblotting. Following conjugation, excess BARAC was removed by ultracentrifugation and washed with 25 mm NH₄HCO₃. Biotin-conjugated cytochrome C was purified through binding to streptavidin beads (15).

As described above, LC-MS^(n) analysis was performed on the acid-cleaved products of Azide-A-DSBSO cross-linked peptides (i.e. DSBSO cross-linked peptides) (FIG. 24A-FIG. 24C). DSBSO is symmetric and contains two sulfoxide groups that result in four C—S bonds. However, only the two outer C—S bonds proximal to the cross-linked lysines can be cleaved during collision-induced dissociation; the two inner C—S bonds cannot undergo fragmentation because of the lack of β hydrogens (FIG. 24A-FIG. 24C). Given that the same types of MS-cleavable C—S bonds are present in both DSBSO and DSSO, the identification of DSBSO cross-linked peptides by MSn should be as robust as that of DSSO cross-linked peptides (36). This is exemplified by a representative MSn analysis of a DSBSO interlinked peptide (α-β) from in vivo cross-linked 293 cells (FIG. 24A-FIG. 24C).

As shown, the cleavage of either of the two MS-cleavable C—S bonds during MS2 analysis leads to the physical separation of the two DSBSO cross-linked peptide constituents, α and β, yielding two characteristic fragment ion pairs (i.e. αA/βT and αT/βA) (FIG. 24A). These MS2 fragment ions are composed of single peptide chains with defined mass modifications (alkene (A) and thiol (T) remnants of DSBSO), which are then subjected to MS3 sequencing for easy identification by conventional database searching tools (FIG. 24B) (36).

In addition to MS2 and MS3 data, the MS 1 parent ion information is used to further confirm the identities of cross-linked peptides by matching their measured peptide masses to the theoretical masses of predicted cross-linked peptides (FIG. 24C). In this representative example, integration of the MSn data identified the peptide unambiguously as FANYIDK¹²⁰VR cross-linked to QK¹³⁹QASHAQLGDAYDQEIR, describing a new interprotein interaction between vimentin and neurofilament medium polypeptide protein in human 293 cells.

Profiling PPIs from Intact HEK 293 Cells

In Vivo Azide-A-DSBSO Cross-linking of HEK 293 Cells was performed by growing HEK 293 cells on DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were grown to 80% confluence, trypsinized, washed with PBS, and cross-linked with 2 mm Azide-A-DSBSO in PBS for 1 h with rotation at 37° C. Following quenching of cross-linking reactions by the addition of 125 mm glycine, cells were pelleted and stored at −80° C. after removal of the supernatant. Frozen cell pellets were lysed in 8 m urea lysis buffer and clarified via centrifugation (15).

In order to maximize the information acquired on protein interaction interfaces from in vivo cross-linked HEK 293 cells, three different sample preparation strategies, paths I, II, and III was explored (FIG. 25). Path I describes the direct analysis of cross-linked cells as illustrated in FIG. 23. As shown in FIG. 28A-FIG. 28C, protein cross-linking, BARAC conjugation, and purification of cross-linked products were as effective for in vivo cross-linked cells as for standard proteins. Path II incorporates a subcellular fractionation step before BARAC conjugation, thus dividing cell lysates into four fractions: cytosolic, membrane, nuclear, and insoluble fractions. Immunoblotting analysis revealed that such subcellular fractionation was still possible under our experimental conditions, although there was a marked decrease in the amount of proteins in the cytosolic fraction (FIG. 29A-FIG. 29E).

Nonetheless, BARAC reactions and subsequent purification were also effective for each subcellular fraction (FIG. 29A-FIG. 29E). The third sample preparation strategy (path III) involved sequential filtration of in vivo cross-linked cell lysates through 100-kDa and then 30-kDa cutoff centrifugal filters to remove small and non-cross-linked components (FIG. 25). The two-step filtration was used to recover a wider range of cross-linked proteins larger than 30 kDa and to improve the dynamic range of subsequent MS^(n) analysis. Proteins remaining on the two different membranes were digested, and the resulting peptides were collected for BARAC conjugation and streptavidin enrichment of cross-linked peptides. As shown in FIG. 29E, biotin-conjugation and subsequent enrichment were efficient for peptide digests as well, further suggesting the robustness of copper-free click chemistry using BARAC.

From all of the samples prepared, a total of 938 proteins in our analyses (TABLE 8) were identified, 584 of which were identified with at least one cross-linker modified peptide, amounting to 4812 redundant Azide-A-DSBSO labeled peptides, including dead-end, intralinked, and interlinked peptides. Functional annotation of the 584 proteins revealed that they are localized in various cellular compartments and involved in diverse biological processes (TABLE 9), demonstrating that Azide-A-DSBSO is well suited for capturing PPIs in cells.

Protein-Protein Interaction Network Mapping

In some embodiments, mapping Cross-links to 2.5-Å Nucleosome Crystal Structure was performed by downloading the 2.5-Å nucleosome crystal structure (PDB 3AV1) from the Protein Data Bank, and cross-linked residues were mapped and visualized using PyMOL. Distances were measured from the amino group of lysine side chains, also using PyMOL.

Because of their unique capability for describing PPI interfaces, only interlinked peptides are provided in TABLE 10. In this work, 240 unique interlinked peptides were identified, including 136 intrasubunit and 104 intersubunit interlinks. Using this data, an in vivo PPI network map with 85 protein-protein interactions between 54 proteins was established (FIG. 30). In comparison to existing PPI databases, 50 novel intra- and intersubunit interactions were identified with direct physical evidence at specific amino acid residues. Among them, an interesting one is between two intermediate filament proteins, NFM and VIME, an interaction confirmed by seven unique interlinked peptides representing seven unique K-K linkages (TABLE 10). The identification of interlinked peptides between various domains of NFM and VIME suggests that extensive interaction interfaces exist between these two proteins and potentially implicate VIME involvement in the polymerization or regulation of neurofilament proteins in HEK 293 cells.

It has been reported that VIME co-localizes with neurofilament proteins dynamically during neuronal differentiation, and its co-purification with NFH and NFL has been observed (49). Given the close relationship among the three neurofilament subunits NFL, NFM, and NFH, our findings corroborate well with the known function of vimentin in the development of neurofilaments. In general, identifying intermediate filament protein interactions from the native cellular environment is a major challenge, and therefore the ability to capture and directly identify not only which intermediate filament proteins interact, but at which residues, represents a major step forward in this area of research.

It is noted that the most abundant interactions identified in this work resulted from histones and structural proteins (TABLE 10), most likely attributed to their abundance as previously reported (24). In total, 118 unique cross-linked peptides among the four (H2A, H2B, H3.2, and H4) core histones were identified, with 47 from H2A-H2B, 13 from H2A-H3.2, 10 from H2B-H4, 8 from H2B-H3.2, 4 from H3.2-H4, and 1 from H2A-H4 pairs. Additionally, 35 unique intraprotein interlinked peptides were identified, with 20 from H2B, 11 from H3.2, 3 from H4, and 1 from H2A (TABLE 10). Based on the known nucleosome crystal structures (PDB 3AV1) (FIG. 31A-FIG. 31E), the distances between the identified cross-linked lysines are <26 Å, which is consistent with other cross-linking studies (23, 36), suggesting that Azide-A-DSBSO has an ideal spacer length for studying protein structures. Collectively, these results have demonstrated the feasibility of the Azide-A-DSBSO-based XL-MS strategy for mapping PPI network topologies from intact cells.

Mapping In Vivo Subunit Interactions of Proteasome Complexes

In order to establish an in vivo XL-MS workflow for protein complexes (FIG. 23), the Azide-A-DSBSO cross-linking strategy to study interactions of proteasome complexes was employed. To capture and isolate proteasome interacting proteins, 293 cell lines stably expressing an HB-tagged proteasome subunit (i.e. Rpn11-HB or HB-Rpt6) was used. In some embodiments, in vivo cross-linking of HB-tagged proteasome complexes was optimized. As shown in FIG. 32A and FIG. 32B, in vivo Azide-A-DSBSO cross-linking of human proteasome complexes and their subsequent HB-tag-based purification were effective. The BARAC conjugation and enrichment of cross-linked peptides was carried out after purification of in vivo cross-linked proteasome complexes as illustrated in FIG. 23 (path II).

FIG. 26A-FIG. 26D illustrate a representative MSn analysis of an in vivo intersubunit interlinked peptide (m/z 659.82594+) from human proteasome complexes. MS2 analysis of this peptide yielded three detectable fragments, αA (m/z 499.272+), βA (m/z 720.372+), and βT (m/z 811.372+), displaying characteristic fragmentation of DSBSO interlinked peptides. Together with MS3 sequencing of αA (m/z 499.272+) and βT (m/z 811.372+) fragments, MSn analysis identified this cross-linked peptide as NELNAK55VR interlinked to EFLHAQEEVK8OR unambiguously, which represents an intersubunit interaction between proteasome subunits Rpt6:K55 and Rpt3:K80.

In total, MS3 sequencing identified 119 non-redundant cross-linker modified peptides, 54 of which represent 27 unique interlinked peptides (TABLE 11 and TABLE 12). Among them, 22 unique interlinked peptides resulted from inter- or intrasubunit cross-links between known subunits of the proteasome complex, including 8 unique intersubunit (i.e. α3-Rpt6, Rpt2-Rpt6, Rpt3-Rpt6, Rpt4-Rpt6, Rpn5-Rpn6, Rpn11-Rpt6, Rpn5-Rpn9, Rpn2-Rpt6) and 11 unique intrasubunit interactions (TABLE 11 and TABLE 12). In addition to interactions between proteasome subunits, one interprotein interlink between HSPA1A and HSP8A and three intraprotein interlinked peptides from three known proteasome interacting proteins, HSPA1A, EEF2, and RPS15 were identified. In some embodiments, these results demonstrate that the new XL-MS workflow disclosed herein can be generalized to determine protein interaction interfaces of protein complexes in cells.

Biotin Conjugation and Enrichment Strategy for Azide-A-DSBSO Cross Linked Proteins

Azide-A-DSBSO cross-linked 293 cell lysate was reacted with varying concentrations of BARAC with agitation overnight. The resulting biotin-conjugated lysates were analyzed via SDS-PAGE and immunoblot analysis to determine the conjugation efficiency. Bound proteins were reduced with 2 mm tris(2-carboxyethyl)phosphine for 30 min at room temperature and alkylated using 50 mm chloroacetamide in the dark at room temperature for 30 min prior to overnight digestion with 2% Lys-C (w/w) at 37° C. and subsequent overnight digestion with 2% trypsin TPCK (w/w) at 37° C. The Lys-C/trypsin combination is preferred for proteins purified under fully denaturing conditions to achieve optimal digestion efficiency. Non-cross-linked peptides were extracted and analyzed directly via LC-MS/MS, whereas streptavidin-bound peptides were first acid-cleaved from beads with 20% formic acid, 20% acetonitrile overnight before LC-MSn analysis.

Biotin Conjugation and Enrichment Strategy for Azide-A-DSBSO Cross-Linked Peptides

In vivo cross-linked proteins in 293 cell lysates were concentrated using 100-kDa NMWL Amicon Ultra centrifugal filters, and the resulting filtrates were then passed through 30-kDa NMWL Amicon Ultra centrifugal filters. Proteins remaining on both membranes were reduced with 2 mm tris(2-carboxyethyl)phosphine for 30 min at room temperature and then alkylated with 50 mm chloroacetamide at room temperature in the dark for 30 min prior to a 3% Lys-C (w/w) overnight digestion at 37° C. and subsequent 3% trypsin TPCK (w/w) overnight digestion at 37° C. Digests were collected via centrifugation and reacted with 100 μm BARAC at room temperature with agitation overnight. The biotin-conjugated peptides were then enriched using high-capacity streptavidin agarose resin. Bound peptides were acid-cleaved and then submitted for LC-MSn analysis.

Affinity Purification of In Vivo Azide-A-DSBSO Cross-Linked Proteasome Complexes and Subsequent Enrichment of Cross-Linked Peptides

Stable 293 cell lines expressing an HB tagged proteasome subunit (Rpn11 or Rpt6) were grown to confluence in DMEM containing 10% FBS and 1% Pen/strep. The cells were washed with PBS and cross-linked and quenched as described above. The cells were lysed in 8 m urea denaturing lysis buffer (15). The cleared lysates were subjected to HB-tag-based tandem affinity purification, which involved binding to Ni2+-Sepharose beads followed by binding to streptavidin resins (15). Proteins bound on beads were reduced, alkylated, and then incubated in 250 μm BARAC with rotation at room temperature overnight in 8 m urea buffer. After extensive washing, bound proteins were digested by Lys-C and trypsin (15). The peptides freed into solution during digestion were subjected to further enrichment through binding to Neutravidin resin for 1 h at room temperature, and cross-linked peptides were acid-eluted as described. The enriched cross-linked peptides were then subjected to LC-MSn analysis.

Analysis of Cross-Linked Peptides by LC-MSn

Most of the enriched cross-linked peptides were analyzed via LC-MSn using an LTQ-Orbitrap XL mass spectrometer (Thermo Scientific, San Jose, Calif.) coupled on-line with either an Eksigent NanoLC system (Dublin, Calif.) or an EASY-nLC-1000 (Thermo Scientific, San Jose, Calif.). A few cross-linked samples from intact cells were analyzed using an Orbitrap Elite mass spectrometer (courtesy of Thermo Scientific Demo Lab, San Jose, Calif.) coupled on-line with an EASY-nLC 1000 (Thermo Scientific). LC-MSn data acquisition and analysis were as described (20). Only ions with charge of 3+ or more in the MS 1 scan were selected for MS2 analysis.

Identification of Cross-Linked Peptides via Database Searching

Because of the similarity between DSBSO and DSSO, the general data analysis workflow for the identification of DSBSO interlinked peptides via LC-MSn is the same as the analysis of DSSO cross-linked peptides (20, 36). Using the Batch-Tag software within a developmental version of Protein Prospector (v5.10.10, University of California San Francisco), MS2 and MS3 spectra were searched against a decoy database consisting of a normal Swiss-Prot database concatenated with its randomized version (SwissProt.2013.3.1.random.concat with a total of 454,402 protein entries). Homo sapiens was set as the species (20,501 entries) for analyzing data from human cells. The mass tolerances for parent ions and fragment ions were set as ±20 ppm and 0.6 Da, respectively. For Lys-C/trypsin digests, trypsin was set as the enzyme with a maximum of three missed cleavages allowed. Cysteine carbamidomethylation was set as a constant modification. Protein N-terminal acetylation, asparagine deamidation, N-terminal conversion of glutamine to pyroglutamic acid, and methionine oxidation were selected as variable modifications. Similar to DSSO cross-linked peptides, DSBSO cross-linked peptides display unique and characteristic MS2 fragmentation patterns corresponding to their cross-linking types. Therefore, three additional defined modifications on uncleaved lysines and free protein N termini were chosen: alkene (C3H2O, +54 Da), sulfenic acid (C3H4O2S, +254 Da), and unsaturated thiol (C3H2SO, +236 Da). These are modifications resulting from collision-induced dissociation cleavage of the DSBSO cross-linked peptides. Proteins were identified with expectation values ≦0.01 and a minimum of two unique peptides (15).

The in-house program Link-Hunter is a revised version of the previously written Link-Finder program, designed to automatically validate and summarize cross-linked peptide sequences based on MSn data and database searching results as previously described (20, 36). In addition to checking MS2 spectra for predicted patterns, Link-Hunter automatically correlates sequence data from MS3 to MS2 and MS 1 parent masses and reports identified interlinked peptides with two associated sequences.

Interaction Network Mapping and Functional Enrichment Analysis

PPI network graphs resulting from cross-links identified in this work were generated manually in Excel from the final list of identified cross-linked proteins. For comparison with known interactions, the final list of cross-linked interacting proteins was fed into an analysis pipeline that automatically extracts physical (but not genetic) interactions from BioGRID, MINT, and IntAct using their Web services (15). Both PPI networks were imported into and visualized by Cytoscape v2.8.3. Functional enrichment was performed using the DAVID Bioinformatics Resources (v.6.7) Functional Annotation Tool (46). Gene I.D.s were submitted, and the Functional Enrichment Chart with enriched Gene Ontology annotations (cellular compartment and biological processes) was downloaded. Only high-confidence functional annotations (false discovery rate <0.01) were reported.

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Definitions

As used herein, the section headings are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference in their entirety for any purpose. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control. It will be appreciated that there is an implied “about” prior to the temperatures, concentrations, times, etc discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings herein.

Although this invention has been disclosed in the context of certain embodiments and examples, those skilled in the art will understand that the present invention extends beyond the specifically disclosed embodiments to other alternative embodiments and/or uses of the invention and obvious modifications and equivalents thereof. In addition, while several variations of the invention have been shown and described in detail, other modifications, which are within the scope of this invention, will be readily apparent to those of skill in the art based upon this disclosure.

It is also contemplated that various combinations or sub-combinations of the specific features and aspects of the embodiments may be made and still fall within the scope of the invention. It should be understood that various features and aspects of the disclosed embodiments can be combined with, or substituted for, one another in order to form varying modes or embodiments of the disclosed invention. Thus, it is intended that the scope of the present invention herein disclosed should not be limited by the particular disclosed embodiments described above.

It should be understood, however, that this detailed description, while indicating preferred embodiments of the invention, is given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art.

The terminology used in the description presented herein is not intended to be interpreted in any limited or restrictive manner. Rather, the terminology is simply being utilized in conjunction with a detailed description of embodiments of the systems, methods and related components. Furthermore, embodiments may comprise several novel features, no single one of which is solely responsible for its desirable attributes or is believed to be essential to practicing the inventions herein described.

Abbreviations

-   Ac Acetate -   AlkyneA-DSBSO Alkyne-tagged, acid-cleavable     disuccinimiclyl-bissulfoxide -   AzideA-DSBSO Azide-tagged, acid-cleavable     disuccinimidyl-bissulfoxide -   BARAC Biarylazacycloocrynone -   CID Collision-induced dissociation -   CSA Camphorsulfonic acid -   CuAAC Copper(1) catalyzed azide-alkyne cycloaddition -   DIPEA N, N-Diisopropylethylamine -   DMF Dimethylformamide -   DSSO Disuccinimidylsulfoxide -   EDC.HCl. N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide     hydrochloride -   Et₃N Triethylamine -   HB His-bio -   ESI-MS Electrospray ionization-mass spectrometry -   In(OTf)₃ Indium(111) trifluoromethanesulfonate -   K_(A)YIPGTK Lysine(alkene     modified)-tyrosine-isoleucineproline-glycine-threonine-lysine     peptide -   LC/MS Liquid chromatography-mass spectrometry -   MeOH Methanol -   M(ox) Methionine(oxidized)-isoleucine-phenyl -   IFAGIK_(A)K alaninealanine-glycine-isoleucine-lysine(alkene     modified)-lysine -   m-CPBA meta-Chloroperoxybenzoic acid -   MsCl Methanesulfonyl chloride -   NHS N-Hydroxysuccinimiclyl -   Ph-H Benzene -   Pyr. Pyridine -   QTAX Quantitative analysis of tandem affinity purified in vivo     cross-linked (X) protein complexes -   TFAA Trifluoroacetic anhydride -   TFA-NHS N-Trifluoroacetoxy succinimide -   THF Tetrahydrofuran -   TMSCI Trimethylsilyl chloride -   TMSOTf Trimethylsilyl trifluoromethanesulfonate -   TsOH para-Toluenesulfonic acid -   XL-MS Cross-linking mass spectrometry -   μw Microwave -   MS Mass Spectrometry -   MS/MS Tandem Mass Spectrometry -   MS^(n) Multi-Stage Tandem Mass Spectrometry (n=2, 3, . . . ) -   LC MS^(n) Liquid Chromatography Multi-Stage Tandem Mass Spectrometry -   CID Collision Induced Dissociation -   DSSO bis(2,5-dioxopyrrolidin-1-yl) 3,3′-sulfinyldipropanoate -   NMR Nuclear Magnetic Resonance 

1. An MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the MS-cleavable cross-linker comprising: at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group; and at least one collision-induced dissociation (CID) cleavable bond.
 2. The MS-cleavable cross-linker of claim 1, wherein the amine-reactive NHS ester group is designed to react with a lysine side chain in a peptide or a protein.
 3. The MS-cleavable cross-linker of claim 1, wherein the at least one CID cleavable bond is a sulfoxide bond.
 4. The MS-cleavable cross-linker of claim 1, wherein the MS-cleavable cross-linker is DSSO, comprising the structure:


5. The MS-cleavable cross-linker of claim 1, additionally comprising: at least one enrichment handle; and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.
 6. The MS-cleavable cross-linker of claim 5, wherein the at least one enrichment handle comprises a functional group, wherein the functional group is an azide functional group or an alkyne functional group, and wherein the functional group is designed for a click reaction with strained alkynes or a CuAAC reaction.
 7. The MS-cleavable cross-linker of claim 5, wherein the acid cleavable site is an acid labile acetal bond, wherein the acid labile acetal bond is designed to be cleaved under aqueous acidic conditions.
 8. The MS-cleavable cross-linker of claim 5, wherein the MS-cleavable cross-linker is azide-A-DSBDO, comprising the structure:


9. The MS-cleavable cross-linker of claim 5, wherein the MS-cleavable cross-linker is alkyne-A-DSBDO, comprising the structure:


10. A method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the method comprising the steps of: (i) providing 3,3′-thiodipropionic acid; (ii) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-thiodipropionate from the compound of step (i); and (iii) deriving DSSO from the compound of step (ii).
 11. A method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the method comprising the steps of: (i) providing 2,2-bis(hydroxymethyl)propane-1,3-diol; (ii) deriving (1,5-dioxaspiro[5.5]undecane-3,3-diyl)dimethanol from the compound of step (i); (iii) deriving (1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene) dimethanesulfonate from the compound of step (ii); (iv) deriving S,S′-((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene)) diethanethioate from the compound of step (iii); (v) deriving dimethyl 3,3′-(((1,5-dioxaspiro[5.5]undecane-3,3-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (iv); (vi) deriving dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate from the compound of step (v); (vii) deriving dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (vi); (viii) deriving 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionic acid from the compound of step (vii); (ix) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (viii); (x) deriving azide-A-DSBDO from the compound of step (ix).
 12. A method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the method comprising the steps of: (i) providing 2,2-bis(bromomethyl)propane-1,3-diol and methyl 3-mercaptopropanoate; (ii) deriving dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate from the compounds of step (i); (iii) deriving dimethyl 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (ii); (iv) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(3-azidopropyl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (iii); and (v) deriving azide-A-DSBDO from the compound of step (iv).
 13. A method for synthesis of an MS-cleavable cross-linker for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the method comprising the steps of: (i) providing dimethyl 3,3′-((2,2-bis(hydroxymethyl)propane-1,3-diyl)bis(sulfanediyl))dipropionate; (ii) deriving dimethyl 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionate from the compound of step (i); (iii) deriving bis(2,5-dioxopyrrolidin-1-yl) 3,3′-(((2-(but-3-yn-1-yl)-2-methyl-1,3-dioxane-5,5-diyl)bis(methylene))bis(sulfanediyl))dipropionatefrom the compound of step (ii); and (iv) deriving alkyne-A-DSBDO from the compound of step (iii).
 14. A method for mapping intra-protein interactions in a protein, inter-protein interactions in a protein complex or a combination thereof, the method comprising: providing an MS-cleavable cross-linker, wherein the MS-cleavable cross-linker comprises: at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group, and at least one collision-induced dissociation (CID) cleavable bond; forming a cross-linked protein or protein complex by cross-linking the protein or the protein complex with the MS-cleavable cross-linker; forming one or more peptide fragments that are chemically bound to the MS-cleavable cross-linker by digesting the cross-linked protein or protein complex with an enzyme; and identifying the one or more peptide fragments using tandem mass spectrometry (MS^(n)), thereby mapping intra-protein interactions in a protein and inter-protein interactions in a protein complex.
 15. The method of claim 14, wherein the MS-cleavable cross-linking agent is a derivative of a compound of structure:

wherein X is selected from the group consisting of:

wherein R is H, methyl or ethyl.
 16. The method of claim 14, wherein the MS-cleavable cross-linking agent is DSSO, comprising the structure:


17. The method of claim 14, wherein the MS-cleavable cross-linking agent additionally comprises: at least one enrichment handle; and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.
 18. The method of claim 17, wherein the MS-cleavable cross-linking agent is azide-A-DSBSO, comprising the structure:


19. The method of claim 17, wherein the MS-cleavable cross-linking agent is alkyne-A-DSBSO, comprising the structure:


20. The method of claim 17, wherein the at least one enrichment handle comprises a functional group for an enrichment strategy, wherein the functional group is an azide functional group or an alkyne functional group, and wherein the functional group is designed for a click reaction with strained alkynes or a CuAAC reaction.
 21. The method of claim 20, wherein the enrichment strategy is an affinity purification wherein the affinity purification comprises direct coupling with alkyne or azide functionalized beads or linking with one or more common affinity ligands such as biotin.
 22. The method of claim 17, wherein the acid cleavable site is an acid labile acetal bond, wherein the acid labile acetal bond is designed to be cleaved under aqueous acidic conditions for selective elution from an affinity column.
 23. A method for cross-linking mass spectrometry (XL-MS) for identifying one or more cross-linked peptides, the method comprising: performing cross-linking with an MS-cleavable cross-linker to obtain one or more cross-linked proteins, wherein the MS-cleavable cross-linker comprises: at least one amine-reactive N-hydroxysuccinimdyl (NHS) ester group, and at least one collision-induced dissociation (CID) cleavable bond; digesting the one or more cross-linked proteins with trypsin to obtain one or more cross-linked peptides; performing a liquid chromatography-tandem mass spectrometry (LC-MS″) analysis on the one or more cross-linked peptides, wherein the LC-MSn analysis comprises: detecting the one or more cross-linked peptides by MS 1 analysis; selecting the one or more cross-linked peptides detected by MS 1 for MS2 analysis; selectively fragmenting the at least one CID cleavable bond and separating the one or more cross-linked peptides during MS2 analysis; sequencing the one or more cross-linked peptides separated during MS2 analysis by MS3 analysis; and integrating data obtained during MS 1, MS2 and MS3 analyses to identify the one or more cross-linked peptides.
 24. The method of claim 23, wherein the MS-cleavable cross-linking agent is DSSO, comprising the structure:


25. The method of claim 23, wherein the MS-cleavable cross-linking agent additionally comprises: at least one enrichment handle; and at least one acid cleavage site, wherein the MS-cleavable cross-linker is membrane permeable.
 26. The method of claim 25, wherein the MS-cleavable cross-linking agent is azide-A-DSBSO, comprising the structure:


27. The method of claim 25, wherein the MS-cleavable cross-linking agent is alkyne-A-DSBSO, comprising the structure: 